Mercurial > repos > bgruening > hicexplorer_hicpca

annotate macros.xml @ 3:02c7b035c9f6 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 02:30:11 -0500
parents a5b031cbf3f8
children 8682a17173fb
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e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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1 <macros>
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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02c7b035c9f6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
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3 <token name="@WRAPPER_VERSION@">2.1</token>
02c7b035c9f6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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iuc
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5 <token name="@USE_RANGE@">
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6 #if $use_range.select_use_range == "yes_use_range":
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7 --range $range_min:$range_max
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8 #end if
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9 </token>
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
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14 <yield />
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15 </requirements>
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16 <version_command>@BINARY@ --version</version_command>
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17 </xml>
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19 <xml name="citations">
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20 <citations>
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21 <citation type="doi">10.5281/zenodo.1133705</citation>
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22 <yield />
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23 </citations>
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24 </xml>
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26 <xml name="zMax">
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27 <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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28 </xml>
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29 <xml name="use_range">
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30 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
02c7b035c9f6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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31 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
02c7b035c9f6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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32 <option value="no_use_range">No restriction</option>
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33 <option value="yes_use_range">Only consider counts within a range</option>
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34 </param>
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35 <when value="no_use_range"/>
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36 <when value="yes_use_range">
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37 <expand macro='range' />
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38 </when>
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39 </conditional>
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40 </xml>
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41
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42 <xml name="range">
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43 <param name="range_min" type="integer" value="" min="0"/>
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44 <param name="range_max" type="integer" value="" min="0"/>
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45 </xml>
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46
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47 <xml name="colormap">
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48 <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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49 <option value="RdYlBu">RdYlBu</option>
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50 <option value="Accent">Accent</option>
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51 <option value="Spectral">Spectral</option>
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52 <option value="Set1">Set1</option>
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53 <option value="Set2">Set2</option>
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54 <option value="Set3">Set3</option>
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55 <option value="Dark2">Dark2</option>
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56 <option value="Reds">Reds</option>
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57 <option value="Oranges">Oranges</option>
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58 <option value="Greens">Greens</option>
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59 <option value="Blues">Blues</option>
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60 <option value="Greys">Greys</option>
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61 <option value="Purples">Purples</option>
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62 <option value="Paired">Paired</option>
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63 <option value="Pastel1">Pastel1</option>
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64 <option value="Pastel2">Pastel2</option>
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65 <option value="spring">spring</option>
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66 <option value="summer">summer</option>
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67 <option value="autumn">autumn</option>
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68 <option value="winter">winter</option>
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69 <option value="hot">hot</option>
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70 <option value="coolwarm">coolwarm</option>
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71 <option value="cool">cool</option>
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72 <option value="seismic">seismic</option>
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73 <option value="terrain">terrain</option>
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74 <option value="ocean">ocean</option>
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75 <option value="rainbow">rainbow</option>
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76 <option value="bone">bone</option>
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77 <option value="flag">flag</option>
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78 <option value="prism">prism</option>
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79 <option value="cubehelix">cubehelix</option>
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80 <option value="binary">binary</option>
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81 <option value="pink">pink</option>
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82 <option value="gray">gray</option>
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83 <option value="copper">copper</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
84 <option value="BrBG">BrBG</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
85 <option value="BuGn">BuGn</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
86 <option value="BuPu">BuPu</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
87 <option value="GnBu">GnBu</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
88 <option value="OrRd">OrRd</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
89 <option value="PiYG">PiYG</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
90 <option value="PRGn">PRGn</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
91 <option value="PuOr">PuOr</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
92 <option value="PuRd">PuRd</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
93 <option value="PuBu">PuBu</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
94 <option value="RdBu">RdBu</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
95 <option value="RdGy">RdGy</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
96 <option value="RdPu">RdPu</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
97 <option value="YlGn">YlGn</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
98 <option value="PuBuGn">PuBuGn</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
99 <option value="RdYlGn">RdYlGn</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
100 <option value="YlGnBu">YlGnBu</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
101 <option value="YlOrBr">YlOrBr</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
102 <option value="YlOrRd">YlOrRd</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
103 <option value="gist_gray">gist_gray</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
104 <option value="gist_stern">gist_stern</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
105 <option value="gist_earth">gist_earth</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
106 <option value="gist_yarg">gist_yarg</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
107 <option value="gist_ncar">gist_ncar</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
108 <option value="gist_rainbow">gist_rainbow</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
109 <option value="gist_heat">gist_heat</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
110 <option value="gnuplot">gnuplot</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
111 <option value="gnuplot2">gnuplot2</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
112 <option value="CMRmap">CMRmap</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
113 <option value="bwr">bwr</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
114 <option value="hsv">hsv</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
115 <option value="brg">brg</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
116 <option value="jet">jet</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
117 <option value="afmhot">afmhot</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
118 <option value="Accent_r">Accent reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
119 <option value="Spectral_r">Spectral reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
120 <option value="Set1_r">Set1 reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
121 <option value="Set2_r">Set2 reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
122 <option value="Set3_r">Set3 reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
123 <option value="Dark2_r">Dark2 reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
124 <option value="Reds_r">Reds reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
125 <option value="Oranges_r">Oranges reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
126 <option value="Greens_r">Greens reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
127 <option value="Blues_r">Blues reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
128 <option value="Greys_r">Greys reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
129 <option value="Purples_r">Purples reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
130 <option value="Paired_r">Paired reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
131 <option value="Pastel1_r">Pastel1 reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
132 <option value="Pastel2_r">Pastel2 reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
133 <option value="spring_r">spring reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
134 <option value="summer_r">summer reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
135 <option value="autumn_r">autumn reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
136 <option value="winter_r">winter reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
137 <option value="hot_r">hot reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
138 <option value="coolwarm_r">coolwarm reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
139 <option value="cool_r">cool reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
140 <option value="seismic_r">seismic reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
141 <option value="terrain_r">terrain reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
142 <option value="ocean_r">ocean reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
143 <option value="rainbow_r">rainbow reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
144 <option value="bone_r">bone reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
145 <option value="flag_r">flag reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
146 <option value="prism_r">prism reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
147 <option value="cubehelix_r">cubehelix reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
148 <option value="binary_r">binary reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
149 <option value="pink_r">pink reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
150 <option value="gray_r">gray reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
151 <option value="copper_r">copper reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
152 <option value="BrBG_r">BrBG reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
153 <option value="BuGn_r">BuGn reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
154 <option value="BuPu_r">BuPu reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
155 <option value="GnBu_r">GnBu reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
156 <option value="OrRd_r">OrRd reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
157 <option value="PiYG_r">PiYG reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
158 <option value="PRGn_r">PRGn reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
159 <option value="PuOr_r">PuOr reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
160 <option value="PuRd_r">PuRd reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
161 <option value="PuBu_r">PuBu reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
162 <option value="RdBu_r">RdBu reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
163 <option value="RdGy_r">RdGy reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
164 <option value="RdPu_r">RdPu reversed</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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165 <option value="YlGn_r">YlGn reversed</option>
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166 <option value="PuBuGn_r">PuBuGn reversed</option>
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167 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
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168 <option value="RdYlGn_r">RdYlGn reversed</option>
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169 <option value="YlGnBu_r">YlGnBu reversed</option>
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170 <option value="YlOrBr_r">YlOrBr reversed</option>
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171 <option value="YlOrRd_r">YlOrRd reversed</option>
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172 <option value="gist_gray_r">gist_gray reversed</option>
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173 <option value="gist_stern_r">gist_stern reversed</option>
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174 <option value="gist_earth_r">gist_earth reversed</option>
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175 <option value="gist_yarg_r">gist_yarg reversed</option>
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176 <option value="gist_ncar_r">gist_ncar reversed</option>
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177 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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178 <option value="gist_heat_r">gist_heat reversed</option>
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179 <option value="gnuplot_r">gnuplot reversed</option>
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180 <option value="gnuplot2_r">gnuplot2 reversed</option>
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181 <option value="CMRmap_r">CMRmap reversed</option>
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182 <option value="bwr_r">bwr reversed</option>
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183 <option value="hsv_r">hsv reversed</option>
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184 <option value="brg_r">brg reversed</option>
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185 <option value="jet_r">jet reversed</option>
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186 <option value="afmhot_r">afmhot reversed</option>
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187 </param>
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188 </xml>
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189
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190
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191 <xml name="multiple_input_matrices">
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192 <repeat name="input_files" title="HiC Matrix files" min="2">
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193 <param name="matrix" type="data" format="h5,cool"
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194 label="HiC Matrix file"
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195 help=""/>
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196 <param name="mlabel" type="text" size="30" optional="true" value=""
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197 label="Label"
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198 help="Label to use in the output. If not given the dataset name will be used instead."/>
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199 </repeat>
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200 </xml>
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201
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202 <token name="@multiple_input_matrices@">
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203 #set $matrices = []
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204 #set $mlabels = []
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205 #for $counter, $i in enumerate($input_files):
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206 ln -s $i.matrix #echo str($counter)+'_matrix'#;
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207 #silent $matrices.append( '%s_matrix' % $counter )
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208
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209 #if str($i.mlabel.value) != "":
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210 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
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211 #else
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212 #set $mlabels += ['"%s"' % ($i.matrix.name)]
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213 #end if
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214 #end for
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215 #set $mlabels = ' '.join($mlabels)
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216 #set $matrices = ' '.join($matrices)
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217 </token>
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218
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219
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220 <xml name="region">
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221 <param name="region" type="text" label="Region of the genome to limit the operation"
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222 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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223 </xml>
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224
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225
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226
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227 <xml name="kmeans_clustering">
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228 <conditional name="used_multiple_regions">
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229 <param name="used_multiple_regions_options" type="select"
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230 label="Did you compute the matrix with more than one groups of regions?"
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231 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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232 <option value="yes">Yes, I used multiple groups of regions</option>
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233 <option value="no">No, I used only one group</option>
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234 </param>
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235 <when value="no">
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236 <conditional name="clustering">
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237 <param name="clustering_options" type="select" label="Clustering algorithm">
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238 <option value="none">No clustering</option>
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239 <option value="kmeans">Kmeans clustering</option>
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240 </param>
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241 <when value="kmeans">
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242 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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243 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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244 </when>
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245 <when value="none" />
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246 </conditional>
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247 </when>
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248 <when value="yes" />
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249 </conditional>
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250 </xml>
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251
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252 <token name="@KMEANS_CLUSTERING@">
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253 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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254 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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255 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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256 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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257 #end if
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258 #end if
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259 #end if
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260 </token>
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261
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262 <xml name="samFlag">
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263 <param name="samFlag" type="integer" optional="true" value=""
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264 label="Filter reads based on the SAM flag"
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265 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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266 </xml>
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267 <xml name="plotNumbers">
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268 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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269 label="Plot the correlation value"
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270 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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271 </xml>
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272 <xml name="doNotExtendPairedEnds">
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273 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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274 label="Do not extend paired ends"
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275 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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276 </xml>
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277
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278 <xml name="ignoreDuplicates">
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279 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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280 label="Ignore duplicates"
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281 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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282 </xml>
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283
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284 <xml name="minMappingQuality">
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285 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
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286 label="Minimum mapping quality"
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287 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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288 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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289 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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290 </xml>
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291
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292 <xml name="skipZeros">
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293 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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294 label ="Skip zeros"
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295 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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296 </xml>
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297
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298 <xml name="fragmentLength">
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299 <param name="fragmentLength" type="integer" value="300" min="1"
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300 label="Fragment length used for the sequencing"
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301 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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302 </xml>
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303
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304 <xml name="scaleFactor">
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305 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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306 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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307 </xml>
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308
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309 <xml name="xMax">
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310 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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311 label="Max value for the x-axis in counts per bin" />
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312 </xml>
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313
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314 <xml name="filterThreshold">
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315 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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316 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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317
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318 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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319 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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320 </xml>
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321
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322
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323 <xml name="pseudocount">
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324 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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325 </xml>
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326 <xml name='matrix_h5_cooler_macro'>
3
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327 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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328 label="Matrix to compute on"/>
0
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329 </xml>
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330 <xml name='matrix_h5_cooler_multiple_macro'>
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331 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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332 label="Matricies to compute on" multiple="true"/>
0
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333 </xml>
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334 <token name="@REFERENCES@">
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335
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336 .. class:: infomark
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337
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338 For more information on the tools, please visit our `help site`_.
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339
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340 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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341
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342 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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343
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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344 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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345 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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346 .. _help site: https://hicexplorer.readthedocs.org
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347
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348 </token>
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349
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350
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351 <xml name="multiple_input_bams">
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352 <repeat name="input_files" title="BAM files" min="2">
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353 <param name="bamfile" type="data" format="bam"
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354 label="Bam file"
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355 help="The BAM file must be sorted."/>
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356 <param name="label" type="text" size="30" optional="true" value=""
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357 label="Label"
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358 help="Label to use in the output. If not given the dataset name will be used instead."/>
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359 </repeat>
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360 </xml>
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361
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362 <xml name="multiple_input_bigwigs">
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363 <repeat name="input_files" title="BigWig files" min="2">
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364 <param name="bigwigfile" type="data" format="bigwig"
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365 label="Bigwig file"
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366 help="The Bigwig file must be sorted."/>
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367 <param name="label" type="text" size="30" optional="true" value=""
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368 label="Label"
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369 help="Label to use in the output. If not given the dataset name will be used instead."/>
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370 </repeat>
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371 </xml>
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372
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373 <xml name="plotTitle">
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374 <param name="plotTitle" type="text" value="" size="30" optional="True"
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375 label="Title of the plot"
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376 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
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377 </xml>
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378
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379 <token name="@multiple_input_bams@">
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380 #import tempfile
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381 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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382 #set files=[]
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383 #set labels=[]
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384 #for $i in $input_files:
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385 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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386 #set $temp_input_path = $temp_input_handle.name
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387 #silent $temp_input_handle.close()
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388 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
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389 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
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390 #silent $files.append('%s.bam' % $temp_input_path)
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391
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392 ##set $files += [str($i.bamfile)]
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393 #if str($i.label.value) != "":
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394 #set $labels += ["\"%s\"" % ($i.label.value)]
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395 #else
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396 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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397 #end if
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398 #end for
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399 </token>
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400
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401 <token name="@multiple_input_bigwigs@">
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402 #import tempfile
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403 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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404 #set files=[]
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405 #set labels=[]
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406 #for $i in $input_files:
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407 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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408 #set $temp_input_path = $temp_input_handle.name
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409 #silent $temp_input_handle.close()
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410 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
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411 #silent $files.append('%s.bw' % $temp_input_path)
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412
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413 ##set $files += [str($i.bigwigfile)]
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414 #if str($i.label.value) != "":
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415 #set $labels += ["\"%s\"" % ($i.label.value)]
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416 #else
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417 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
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418 #end if
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419 #end for
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420 </token>
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421
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422 <xml name="reference_genome_source">
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423 <conditional name="source">
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424 <param name="ref_source" type="select" label="Reference genome">
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425 <option value="cached">locally cached</option>
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426 <option value="history">in your history</option>
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427 </param>
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428 <when value="cached">
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429 <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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430 <options from_data_table="deepTools_seqs">
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431 <filter type="sort_by" column="1" />
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432 <validator type="no_options" message="No indexes are available." />
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433 </options>
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434 </param>
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435 </when>
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436 <when value="history">
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437 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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438 </when>
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439 </conditional>
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440 </xml>
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441
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442 <token name="@reference_genome_source@">
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443 #if $source.ref_source=="history":
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444 --genome $source.input1
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445 #else:
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446 --genome "${source.input1_2bit.fields.path}"
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447 #end if
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448 </token>
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449
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450 <xml name="effectiveGenomeSize">
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451 <conditional name="effectiveGenomeSize">
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452 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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453 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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454 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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455 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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456 <option value="93260000">ce10 (93260000)</option>
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457 <option value="121400000">dm3 (121400000)</option>
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458 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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459 <option value="2150570000">mm9 (2150570000)</option>
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460 <option value="specific">user specified</option>
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461 </param>
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462 <when value="specific">
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463 <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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464 </when>
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465 <when value="2150570000" />
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466 <when value="2451960000" />
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467 <when value="121400000" />
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468 <when value="93260000" />
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469 </conditional>
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470 </xml>
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471
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472 <xml name="image_file_format">
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473 <param name="outFileFormat" type="select" label="Image file format">
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474 <option value="png" selected="true">png</option>
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475 <option value="pdf">pdf</option>
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476 <option value="svg">svg</option>
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477 <option value="eps">eps</option>
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478 <option value="emf">emf</option>
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479 </param>
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480 </xml>
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481
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482 <xml name="missingDataAsZero">
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483 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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484 label ="Treat missing data as zero"
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485 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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486 </xml>
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487
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488 <xml name="input_save_matrix_values">
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489 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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490 </xml>
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491
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492 <xml name="input_graphic_output_settings">
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493 <conditional name="output" >
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494 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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495 <option value="no" selected="true">no</option>
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496 <option value="yes">yes</option>
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497 </param>
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498 <when value="no" />
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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499 <when value="yes">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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500 <yield />
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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501 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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502 <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."/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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503 </when>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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504 </conditional>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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505 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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506
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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507 <xml name="input_image_file_format">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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508 <param name="outFileFormat" type="select" label="Image file format">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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509 <option value="png" selected="true">png</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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510 <option value="pdf">pdf</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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511 <option value="svg">svg</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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512 <option value="eps">eps</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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513 <option value="emf">emf</option>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
514 </param>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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515 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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516
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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517 <xml name="output_image_file_format">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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518 <data format="png" name="outFileName" label="${tool.name} image">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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519 <change_format>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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520 <when input="output.outFileFormat" value="pdf" format="pdf" />
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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521 <when input="output.outFileFormat" value="svg" format="svg" />
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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522 <when input="output.outFileFormat" value="eps" format="eps" />
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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523 <when input="output.outFileFormat" value="emf" format="emf" />
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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524 </change_format>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
525 </data>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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526 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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527
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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528 <xml name="output_save_matrix_values">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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529 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
530 <filter>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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531 ((
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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532 output['showOutputSettings'] == 'yes' and
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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533 output['saveMatrix'] is True
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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534 ))
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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535 </filter>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
536 </data>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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537 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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538
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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539 <xml name="output_graphic_outputs">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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540 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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541 <filter>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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542 ((
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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543 output['showOutputSettings'] == 'yes' and
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
544 output['saveData'] is True
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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545 ))
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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546 </filter>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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547 </data>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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548 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
549 <filter>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
550 ((
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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551 output['showOutputSettings'] == 'yes' and
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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552 output['saveSortedRegions'] is True
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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553 ))
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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554 </filter>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
555 </data>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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556 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
557
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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558 <xml name="track_input_h5_macro">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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559 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
560 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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561 <xml name="track_input_bed_macro">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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562 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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563 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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564 <xml name="track_input_bedgraph_macro">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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565 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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566 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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567 <xml name="track_input_bigwig_macro">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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568 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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569 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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570 <xml name="track_input_bedgraph_matrix_macro">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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571 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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572 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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573 <xml name="track_input_tabular_macro">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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574 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
575 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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576 <xml name="plot_title">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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577 <param name="title" type="text" optional="true" label="Plot title"/>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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578 </xml>
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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579
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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580 <xml name="spacer_macro">
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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581 <param name="spacer_width" type="float" value="" optional="True"
3
02c7b035c9f6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
582 label="Include spacer at the end of the track." help="Width of the spacer." />
0
e3d020b23ad5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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583 </xml>
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584 <xml name="fontsize_macro">
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585 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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586 </xml>
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587 </macros>