annotate macros.xml @ 1:ef86780a77ff draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
author bgruening
date Mon, 03 Apr 2017 07:08:11 -0400
parents fe0243c46b36
children ae2d7e2dfeef
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fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <macros>
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2 <xml name="stdio">
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3 <stdio>
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4 <exit_code range="1:" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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5 <exit_code range=":-1" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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6 <regex match="Error:" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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7 <regex match="Exception:" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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8 <regex match="EXception:" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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9 <regex match="Traceback" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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10 </stdio>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 </xml>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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13 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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ef86780a77ff planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
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14 <token name="@WRAPPER_VERSION@">1.7.2</token>
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15 <xml name="requirements">
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16 <requirements>
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17 <requirement type="package" version="2.7.13">python</requirement>
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18 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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19 <yield />
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20 </requirements>
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21 <expand macro="stdio" />
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22 <version_command>@BINARY@ --version</version_command>
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23 </xml>
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24
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25 <xml name="citations">
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26 <citations>
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27 <citation type="doi">10.5281/zenodo.159780</citation>
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28 <yield />
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29 </citations>
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30 </xml>
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31
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32 <xml name="zMax">
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33 <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 -->
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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34 </xml>
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35
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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36 <xml name="colormap">
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37 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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38 <option value="RdYlBu">RdYlBu</option>
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39 <option value="Accent">Accent</option>
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40 <option value="Spectral">Spectral</option>
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41 <option value="Set1">Set1</option>
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42 <option value="Set2">Set2</option>
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43 <option value="Set3">Set3</option>
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44 <option value="Dark2">Dark2</option>
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45 <option value="Reds">Reds</option>
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46 <option value="Oranges">Oranges</option>
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47 <option value="Greens">Greens</option>
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48 <option value="Blues">Blues</option>
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49 <option value="Greys">Greys</option>
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50 <option value="Purples">Purples</option>
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51 <option value="Paired">Paired</option>
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52 <option value="Pastel1">Pastel1</option>
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53 <option value="Pastel2">Pastel2</option>
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54 <option value="spring">spring</option>
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55 <option value="summer">summer</option>
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56 <option value="autumn">autumn</option>
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57 <option value="winter">winter</option>
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58 <option value="hot">hot</option>
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59 <option value="coolwarm">coolwarm</option>
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60 <option value="cool">cool</option>
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61 <option value="seismic">seismic</option>
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62 <option value="terrain">terrain</option>
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63 <option value="ocean">ocean</option>
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64 <option value="rainbow">rainbow</option>
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65 <option value="bone">bone</option>
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66 <option value="flag">flag</option>
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67 <option value="prism">prism</option>
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68 <option value="cubehelix">cubehelix</option>
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69 <option value="binary">binary</option>
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70 <option value="pink">pink</option>
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71 <option value="gray">gray</option>
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72 <option value="copper">copper</option>
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73 <option value="BrBG">BrBG</option>
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74 <option value="BuGn">BuGn</option>
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75 <option value="BuPu">BuPu</option>
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76 <option value="GnBu">GnBu</option>
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77 <option value="OrRd">OrRd</option>
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78 <option value="PiYG">PiYG</option>
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79 <option value="PRGn">PRGn</option>
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80 <option value="PuOr">PuOr</option>
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81 <option value="PuRd">PuRd</option>
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82 <option value="PuBu">PuBu</option>
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83 <option value="RdBu">RdBu</option>
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84 <option value="RdGy">RdGy</option>
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85 <option value="RdPu">RdPu</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
86 <option value="YlGn">YlGn</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
87 <option value="PuBuGn">PuBuGn</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
88 <option value="RdYlGn">RdYlGn</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
89 <option value="YlGnBu">YlGnBu</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
90 <option value="YlOrBr">YlOrBr</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
91 <option value="YlOrRd">YlOrRd</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
92 <option value="gist_gray">gist_gray</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
93 <option value="gist_stern">gist_stern</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
94 <option value="gist_earth">gist_earth</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
95 <option value="gist_yarg">gist_yarg</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
96 <option value="gist_ncar">gist_ncar</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
97 <option value="gist_rainbow">gist_rainbow</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
98 <option value="gist_heat">gist_heat</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
99 <option value="gnuplot">gnuplot</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
100 <option value="gnuplot2">gnuplot2</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
101 <option value="CMRmap">CMRmap</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
102 <option value="bwr">bwr</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
103 <option value="hsv">hsv</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
104 <option value="brg">brg</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
105 <option value="jet">jet</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
106 <option value="afmhot">afmhot</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
107 <option value="Accent_r">Accent reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
108 <option value="Spectral_r">Spectral reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
109 <option value="Set1_r">Set1 reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
110 <option value="Set2_r">Set2 reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
111 <option value="Set3_r">Set3 reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
112 <option value="Dark2_r">Dark2 reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
113 <option value="Reds_r">Reds reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
114 <option value="Oranges_r">Oranges reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
115 <option value="Greens_r">Greens reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
116 <option value="Blues_r">Blues reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
117 <option value="Greys_r">Greys reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
118 <option value="Purples_r">Purples reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
119 <option value="Paired_r">Paired reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
120 <option value="Pastel1_r">Pastel1 reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
121 <option value="Pastel2_r">Pastel2 reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
122 <option value="spring_r">spring reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
123 <option value="summer_r">summer reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
124 <option value="autumn_r">autumn reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
125 <option value="winter_r">winter reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
126 <option value="hot_r">hot reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
127 <option value="coolwarm_r">coolwarm reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
128 <option value="cool_r">cool reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
129 <option value="seismic_r">seismic reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
130 <option value="terrain_r">terrain reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
131 <option value="ocean_r">ocean reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
132 <option value="rainbow_r">rainbow reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
133 <option value="bone_r">bone reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
134 <option value="flag_r">flag reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
135 <option value="prism_r">prism reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
136 <option value="cubehelix_r">cubehelix reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
137 <option value="binary_r">binary reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
138 <option value="pink_r">pink reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
139 <option value="gray_r">gray reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
140 <option value="copper_r">copper reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
141 <option value="BrBG_r">BrBG reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
142 <option value="BuGn_r">BuGn reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
143 <option value="BuPu_r">BuPu reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
144 <option value="GnBu_r">GnBu reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
145 <option value="OrRd_r">OrRd reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
146 <option value="PiYG_r">PiYG reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
147 <option value="PRGn_r">PRGn reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
148 <option value="PuOr_r">PuOr reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
149 <option value="PuRd_r">PuRd reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
150 <option value="PuBu_r">PuBu reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
151 <option value="RdBu_r">RdBu reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
152 <option value="RdGy_r">RdGy reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
153 <option value="RdPu_r">RdPu reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
154 <option value="YlGn_r">YlGn reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
155 <option value="PuBuGn_r">PuBuGn reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
156 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
157 <option value="RdYlGn_r">RdYlGn reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
158 <option value="YlGnBu_r">YlGnBu reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
159 <option value="YlOrBr_r">YlOrBr reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
160 <option value="YlOrRd_r">YlOrRd reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
161 <option value="gist_gray_r">gist_gray reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
162 <option value="gist_stern_r">gist_stern reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
163 <option value="gist_earth_r">gist_earth reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
164 <option value="gist_yarg_r">gist_yarg reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
165 <option value="gist_ncar_r">gist_ncar reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
166 <option value="gist_rainbow_r">gist_rainbow reversed</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
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167 <option value="gist_heat_r">gist_heat reversed</option>
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168 <option value="gnuplot_r">gnuplot reversed</option>
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169 <option value="gnuplot2_r">gnuplot2 reversed</option>
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170 <option value="CMRmap_r">CMRmap reversed</option>
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171 <option value="bwr_r">bwr reversed</option>
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172 <option value="hsv_r">hsv reversed</option>
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173 <option value="brg_r">brg reversed</option>
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174 <option value="jet_r">jet reversed</option>
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175 <option value="afmhot_r">afmhot reversed</option>
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176 </param>
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177 </xml>
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178
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179
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180 <xml name="multiple_input_matrices">
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181 <repeat name="input_files" title="HiC Matrix files" min="2">
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182 <param name="matrix" type="data" format="h5"
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183 label="HiC Matrix file"
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184 help=""/>
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185 <param name="mlabel" type="text" size="30" optional="true" value=""
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186 label="Label"
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187 help="Label to use in the output. If not given the dataset name will be used instead."/>
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188 </repeat>
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189 </xml>
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190
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191 <token name="@multiple_input_matrices@">
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192 #set $matrices = []
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193 #set $mlabels = []
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194 #for $counter, $i in enumerate($input_files):
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195 ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
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196 #silent $matrices.append( '%s.npz.h5' % $counter )
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197
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198 #if str($i.mlabel.value) != "":
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199 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
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200 #else
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201 #set $mlabels += ['"%s"' % ($i.matrix.name)]
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202 #end if
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203 #end for
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204 #set $mlabels = ' '.join($mlabels)
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205 #set $matrices = ' '.join($matrices)
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206 </token>
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207
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208
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209 <xml name="region">
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210 <param name="region" type="text" label="Region of the genome to limit the operation"
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211 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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212 </xml>
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213
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214
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215
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216 <xml name="kmeans_clustering">
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217 <conditional name="used_multiple_regions">
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218 <param name="used_multiple_regions_options" type="select"
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219 label="Did you compute the matrix with more than one groups of regions?"
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220 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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221 <option value="yes">Yes, I used multiple groups of regions</option>
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222 <option value="no">No, I used only one group</option>
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223 </param>
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224 <when value="no">
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225 <conditional name="clustering">
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226 <param name="clustering_options" type="select" label="Clustering algorithm">
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227 <option value="none">No clustering</option>
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228 <option value="kmeans">Kmeans clustering</option>
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229 </param>
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230 <when value="kmeans">
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231 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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232 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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233 </when>
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234 <when value="none" />
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235 </conditional>
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236 </when>
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237 <when value="yes" />
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238 </conditional>
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239 </xml>
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240
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241 <token name="@KMEANS_CLUSTERING@">
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242 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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243 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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244 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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245 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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246 #end if
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247 #end if
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248 #end if
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249 </token>
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250
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251 <xml name="samFlag">
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252 <param name="samFlag" type="integer" optional="true" value=""
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253 label="Filter reads based on the SAM flag"
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254 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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255 </xml>
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256 <xml name="plotNumbers">
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257 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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258 label="Plot the correlation value"
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259 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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260 </xml>
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261 <xml name="doNotExtendPairedEnds">
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262 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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263 label="Do not extend paired ends"
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264 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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265 </xml>
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266
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267 <xml name="ignoreDuplicates">
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268 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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269 label="Ignore duplicates"
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270 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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271 </xml>
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272
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273 <xml name="minMappingQuality">
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274 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
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275 label="Minimum mapping quality"
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276 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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277 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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278 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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279 </xml>
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280
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281 <xml name="skipZeros">
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282 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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283 label ="Skip zeros"
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284 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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285 </xml>
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286
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287 <xml name="fragmentLength">
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288 <param name="fragmentLength" type="integer" value="300" min="1"
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289 label="Fragment length used for the sequencing"
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290 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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291 </xml>
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292
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293 <xml name="scaleFactor">
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294 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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295 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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296 </xml>
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297
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298 <xml name="xMax">
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299 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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300 label="Max value for the x-axis in counts per bin" />
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301 </xml>
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302
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303 <xml name="filterThreshold">
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304 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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305 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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306
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307 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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308 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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309 </xml>
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310
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311
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312 <xml name="pseudocount">
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313 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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314 </xml>
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315
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316 <token name="@REFERENCES@">
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317
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318 .. class:: infomark
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319
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320 For more information on the tools, please visit our `help site`_.
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321
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322 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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323
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324 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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325
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326 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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327 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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328 .. _help site: https://github.com/fidelram/deepTools/wiki/
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329
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330 </token>
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331
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332
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333 <xml name="multiple_input_bams">
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334 <repeat name="input_files" title="BAM files" min="2">
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335 <param name="bamfile" type="data" format="bam"
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336 label="Bam file"
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337 help="The BAM file must be sorted."/>
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338 <param name="label" type="text" size="30" optional="true" value=""
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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339 label="Label"
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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340 help="Label to use in the output. If not given the dataset name will be used instead."/>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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341 </repeat>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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342 </xml>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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343
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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344 <xml name="multiple_input_bigwigs">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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345 <repeat name="input_files" title="BigWig files" min="2">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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346 <param name="bigwigfile" type="data" format="bigwig"
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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347 label="Bigwig file"
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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348 help="The Bigwig file must be sorted."/>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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349 <param name="label" type="text" size="30" optional="true" value=""
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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350 label="Label"
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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351 help="Label to use in the output. If not given the dataset name will be used instead."/>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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352 </repeat>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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353 </xml>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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354
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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355 <xml name="plotTitle">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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356 <param name="plotTitle" type="text" value="" size="30" optional="True"
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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357 label="Title of the plot"
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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358 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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359 </xml>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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360
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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361 <token name="@multiple_input_bams@">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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362 #import tempfile
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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363 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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364 #set files=[]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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365 #set labels=[]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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366 #for $i in $input_files:
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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367 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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368 #set $temp_input_path = $temp_input_handle.name
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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369 #silent $temp_input_handle.close()
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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370 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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371 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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372 #silent $files.append('%s.bam' % $temp_input_path)
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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373
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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374 ##set $files += [str($i.bamfile)]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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375 #if str($i.label.value) != "":
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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376 #set $labels += ["\"%s\"" % ($i.label.value)]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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377 #else
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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378 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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379 #end if
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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380 #end for
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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381 </token>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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382
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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383 <token name="@multiple_input_bigwigs@">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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384 #import tempfile
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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385 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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386 #set files=[]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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387 #set labels=[]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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388 #for $i in $input_files:
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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389 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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390 #set $temp_input_path = $temp_input_handle.name
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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391 #silent $temp_input_handle.close()
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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392 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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393 #silent $files.append('%s.bw' % $temp_input_path)
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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394
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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395 ##set $files += [str($i.bigwigfile)]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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396 #if str($i.label.value) != "":
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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397 #set $labels += ["\"%s\"" % ($i.label.value)]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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398 #else
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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399 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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400 #end if
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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401 #end for
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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402 </token>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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403
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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404 <xml name="reference_genome_source">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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405 <conditional name="source">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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406 <param name="ref_source" type="select" label="Reference genome">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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407 <option value="cached">locally cached</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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408 <option value="history">in your history</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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409 </param>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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410 <when value="cached">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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411 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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412 <options from_data_table="deepTools_seqs">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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413 <filter type="sort_by" column="1" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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414 <validator type="no_options" message="No indexes are available." />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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415 </options>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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416 </param>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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417 </when>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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418 <when value="history">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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419 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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420 </when>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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421 </conditional>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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422 </xml>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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423
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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424 <token name="@reference_genome_source@">
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425 #if $source.ref_source=="history":
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426 --genome $source.input1
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427 #else:
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428 --genome "${source.input1_2bit.fields.path}"
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429 #end if
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430 </token>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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431
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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432 <xml name="effectiveGenomeSize">
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433 <conditional name="effectiveGenomeSize">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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434 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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435 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.
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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436 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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437 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.">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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438 <option value="93260000">ce10 (93260000)</option>
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439 <option value="121400000">dm3 (121400000)</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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440 <option value="2451960000" selected="true">hg19 (2451960000)</option>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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441 <option value="2150570000">mm9 (2150570000)</option>
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442 <option value="specific">user specified</option>
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443 </param>
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444 <when value="specific">
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445 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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446 </when>
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447 <when value="2150570000" />
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448 <when value="2451960000" />
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449 <when value="121400000" />
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450 <when value="93260000" />
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451 </conditional>
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452 </xml>
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453
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454 <xml name="image_file_format">
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455 <param name="outFileFormat" type="select" label="Image file format">
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456 <option value="png" selected="true">png</option>
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457 <option value="pdf">pdf</option>
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458 <option value="svg">svg</option>
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459 <option value="eps">eps</option>
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460 <option value="emf">emf</option>
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461 </param>
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462 </xml>
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463
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464 <xml name="missingDataAsZero">
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465 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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466 label ="Treat missing data as zero"
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467 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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468 </xml>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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469
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470 <xml name="input_save_matrix_values">
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471 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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472 </xml>
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473
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474 <xml name="input_graphic_output_settings">
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475 <conditional name="output" >
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476 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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477 <option value="no" selected="true">no</option>
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478 <option value="yes">yes</option>
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479 </param>
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480 <when value="no" />
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481 <when value="yes">
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482 <yield />
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483 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
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484 <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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485 </when>
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486 </conditional>
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487 </xml>
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488
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489 <xml name="input_image_file_format">
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490 <param name="outFileFormat" type="select" label="Image file format">
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491 <option value="png" selected="true">png</option>
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492 <option value="pdf">pdf</option>
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493 <option value="svg">svg</option>
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494 <option value="eps">eps</option>
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495 <option value="emf">emf</option>
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496 </param>
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497 </xml>
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498
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499 <xml name="output_image_file_format">
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500 <data format="png" name="outFileName" label="${tool.name} image">
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501 <change_format>
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502 <when input="output.outFileFormat" value="pdf" format="pdf" />
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503 <when input="output.outFileFormat" value="svg" format="svg" />
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504 <when input="output.outFileFormat" value="eps" format="eps" />
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505 <when input="output.outFileFormat" value="emf" format="emf" />
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506 </change_format>
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507 </data>
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508 </xml>
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509
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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510 <xml name="output_save_matrix_values">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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511 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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512 <filter>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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513 ((
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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514 output['showOutputSettings'] == 'yes' and
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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515 output['saveMatrix'] is True
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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516 ))
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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517 </filter>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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518 </data>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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519 </xml>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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520
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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521 <xml name="output_graphic_outputs">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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522 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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523 <filter>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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524 ((
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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525 output['showOutputSettings'] == 'yes' and
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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526 output['saveData'] is True
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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527 ))
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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528 </filter>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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529 </data>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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530 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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531 <filter>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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532 ((
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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533 output['showOutputSettings'] == 'yes' and
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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534 output['saveSortedRegions'] is True
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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535 ))
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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536 </filter>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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537 </data>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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538 </xml>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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539
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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540
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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541
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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542 </macros>