annotate macros.xml @ 15:b553d14a7845 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 06:46:07 -0400
parents fe13295d0329
children 4d2f071002b1
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1 <macros>
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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3 <token name="@WRAPPER_VERSION@">3.4.2</token>
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4 <token name="@USE_RANGE@">
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5 #if $use_range.select_use_range == "yes_use_range":
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6 --range $range_min:$range_max
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7 #end if
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8 </token>
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9
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
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13 <yield />
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14 </requirements>
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15 <version_command>@BINARY@ --version</version_command>
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16 </xml>
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18 <token name="@CHROMOSOME_LIST@">
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19 #if $chromosome_list:
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20 #set $chromosomes = []
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21 #for $chrom in $chromosome_list:
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22 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
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23 #end for
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24 #set $chromosome_string = ' '.join($chromosomes)
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25 --chromosomes $chromosome_string
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26 #end if
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27 </token>
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29 <xml name="chromosome_list">
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30 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
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31 <param argument="--chromosomes" type="text" value="" >
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32 <validator type="empty_field" />
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33 </param>
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34 </repeat>
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35 </xml>
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36
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37 <xml name="citations">
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38 <citations>
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39 <citation type="doi">10.5281/zenodo.1133705</citation>
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40 <yield />
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41 </citations>
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42 </xml>
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44 <xml name="zMax">
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45 <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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46 </xml>
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47 <xml name="use_range">
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48 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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49 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
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50 <option value="no_use_range">No restriction</option>
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51 <option value="yes_use_range">Only consider counts within a range</option>
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52 </param>
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53 <when value="no_use_range"/>
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54 <when value="yes_use_range">
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55 <expand macro='range' />
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56 </when>
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57 </conditional>
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58 </xml>
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59
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60 <xml name="range">
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61 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
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62 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
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63 </xml>
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65 <xml name="colormap">
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66 <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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67 <option value="RdYlBu">RdYlBu</option>
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68 <option value="Accent">Accent</option>
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69 <option value="Spectral">Spectral</option>
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70 <option value="Set1">Set1</option>
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71 <option value="Set2">Set2</option>
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72 <option value="Set3">Set3</option>
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73 <option value="Dark2">Dark2</option>
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74 <option value="Reds">Reds</option>
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75 <option value="Oranges">Oranges</option>
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76 <option value="Greens">Greens</option>
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77 <option value="Blues">Blues</option>
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78 <option value="Greys">Greys</option>
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79 <option value="Purples">Purples</option>
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80 <option value="Paired">Paired</option>
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81 <option value="Pastel1">Pastel1</option>
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82 <option value="Pastel2">Pastel2</option>
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83 <option value="spring">spring</option>
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84 <option value="summer">summer</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
85 <option value="autumn">autumn</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
86 <option value="winter">winter</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
87 <option value="hot">hot</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
88 <option value="coolwarm">coolwarm</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
89 <option value="cool">cool</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
90 <option value="seismic">seismic</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
91 <option value="terrain">terrain</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
92 <option value="ocean">ocean</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
93 <option value="rainbow">rainbow</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
94 <option value="bone">bone</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
95 <option value="flag">flag</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
96 <option value="prism">prism</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
97 <option value="cubehelix">cubehelix</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
98 <option value="binary">binary</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
99 <option value="pink">pink</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
100 <option value="gray">gray</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
101 <option value="copper">copper</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
102 <option value="BrBG">BrBG</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
103 <option value="BuGn">BuGn</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
104 <option value="BuPu">BuPu</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
105 <option value="GnBu">GnBu</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
106 <option value="OrRd">OrRd</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
107 <option value="PiYG">PiYG</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
108 <option value="PRGn">PRGn</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
109 <option value="PuOr">PuOr</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
110 <option value="PuRd">PuRd</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
111 <option value="PuBu">PuBu</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
112 <option value="RdBu">RdBu</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
113 <option value="RdGy">RdGy</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
114 <option value="RdPu">RdPu</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
115 <option value="YlGn">YlGn</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
116 <option value="PuBuGn">PuBuGn</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
117 <option value="RdYlGn">RdYlGn</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
118 <option value="YlGnBu">YlGnBu</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
119 <option value="YlOrBr">YlOrBr</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
120 <option value="YlOrRd">YlOrRd</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
121 <option value="gist_gray">gist_gray</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
122 <option value="gist_stern">gist_stern</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
123 <option value="gist_earth">gist_earth</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
124 <option value="gist_yarg">gist_yarg</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
125 <option value="gist_ncar">gist_ncar</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
126 <option value="gist_rainbow">gist_rainbow</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
127 <option value="gist_heat">gist_heat</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
128 <option value="gnuplot">gnuplot</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
129 <option value="gnuplot2">gnuplot2</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
130 <option value="CMRmap">CMRmap</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
131 <option value="bwr">bwr</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
132 <option value="hsv">hsv</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
133 <option value="brg">brg</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
134 <option value="jet">jet</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
135 <option value="afmhot">afmhot</option>
13
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 11
diff changeset
136 <option value="plasma">plasma</option>
0
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
137 <option value="Accent_r">Accent reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
138 <option value="Spectral_r">Spectral reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
139 <option value="Set1_r">Set1 reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
140 <option value="Set2_r">Set2 reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
141 <option value="Set3_r">Set3 reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
142 <option value="Dark2_r">Dark2 reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
143 <option value="Reds_r">Reds reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
144 <option value="Oranges_r">Oranges reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
145 <option value="Greens_r">Greens reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
146 <option value="Blues_r">Blues reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
147 <option value="Greys_r">Greys reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
148 <option value="Purples_r">Purples reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
149 <option value="Paired_r">Paired reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
150 <option value="Pastel1_r">Pastel1 reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
151 <option value="Pastel2_r">Pastel2 reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
152 <option value="spring_r">spring reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
153 <option value="summer_r">summer reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
154 <option value="autumn_r">autumn reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
155 <option value="winter_r">winter reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
156 <option value="hot_r">hot reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
157 <option value="coolwarm_r">coolwarm reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
158 <option value="cool_r">cool reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
159 <option value="seismic_r">seismic reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
160 <option value="terrain_r">terrain reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
161 <option value="ocean_r">ocean reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
162 <option value="rainbow_r">rainbow reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
163 <option value="bone_r">bone reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
164 <option value="flag_r">flag reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
165 <option value="prism_r">prism reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
166 <option value="cubehelix_r">cubehelix reversed</option>
a9050bffb50c 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="binary_r">binary reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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168 <option value="pink_r">pink reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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169 <option value="gray_r">gray reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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170 <option value="copper_r">copper reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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171 <option value="BrBG_r">BrBG reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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172 <option value="BuGn_r">BuGn reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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173 <option value="BuPu_r">BuPu reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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174 <option value="GnBu_r">GnBu reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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175 <option value="OrRd_r">OrRd reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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176 <option value="PiYG_r">PiYG reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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177 <option value="PRGn_r">PRGn reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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178 <option value="PuOr_r">PuOr reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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179 <option value="PuRd_r">PuRd reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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180 <option value="PuBu_r">PuBu reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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181 <option value="RdBu_r">RdBu reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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182 <option value="RdGy_r">RdGy reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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183 <option value="RdPu_r">RdPu reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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184 <option value="YlGn_r">YlGn reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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185 <option value="PuBuGn_r">PuBuGn reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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186 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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187 <option value="RdYlGn_r">RdYlGn reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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188 <option value="YlGnBu_r">YlGnBu reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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189 <option value="YlOrBr_r">YlOrBr reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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190 <option value="YlOrRd_r">YlOrRd reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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191 <option value="gist_gray_r">gist_gray reversed</option>
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192 <option value="gist_stern_r">gist_stern reversed</option>
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193 <option value="gist_earth_r">gist_earth reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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194 <option value="gist_yarg_r">gist_yarg reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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195 <option value="gist_ncar_r">gist_ncar reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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196 <option value="gist_rainbow_r">gist_rainbow reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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197 <option value="gist_heat_r">gist_heat reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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198 <option value="gnuplot_r">gnuplot reversed</option>
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199 <option value="gnuplot2_r">gnuplot2 reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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200 <option value="CMRmap_r">CMRmap reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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201 <option value="bwr_r">bwr reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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202 <option value="hsv_r">hsv reversed</option>
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203 <option value="brg_r">brg reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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204 <option value="jet_r">jet reversed</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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205 <option value="afmhot_r">afmhot reversed</option>
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206 <option value="plasma_r">plasma reversed</option>
0
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207 </param>
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208 </xml>
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209
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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210 <xml name="multiple_input_matrices">
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211 <repeat name="input_files" title="Hi-C Matrix files" min="2">
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212 <param name="matrix" type="data" format="h5,cool"
9
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213 label="Hi-C Matrix file"
0
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214 help=""/>
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215 <param name="mlabel" type="text" size="30" optional="true" value=""
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216 label="Label"
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217 help="Label to use in the output. If not given the dataset name will be used instead."/>
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218 </repeat>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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219 </xml>
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220
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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221 <token name="@multiple_input_matrices@">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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222 #set $matrices = []
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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223 #set $mlabels = []
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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224 #for $counter, $i in enumerate($input_files):
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225 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
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226 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
0
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227
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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228 #if str($i.mlabel.value) != "":
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229 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
0
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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230 #else
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231 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
0
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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232 #end if
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233 #end for
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234 #set $mlabels = ' '.join($mlabels)
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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235 #set $matrices = ' '.join($matrices)
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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236 </token>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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237
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238 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
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239 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
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240 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
0
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241
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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242 <xml name="region">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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243 <param name="region" type="text" label="Region of the genome to limit the operation"
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244 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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245 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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246
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247
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248
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249 <xml name="kmeans_clustering">
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250 <conditional name="used_multiple_regions">
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251 <param name="used_multiple_regions_options" type="select"
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252 label="Did you compute the matrix with more than one groups of regions?"
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253 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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254 <option value="yes">Yes, I used multiple groups of regions</option>
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255 <option value="no">No, I used only one group</option>
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256 </param>
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257 <when value="no">
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258 <conditional name="clustering">
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259 <param name="clustering_options" type="select" label="Clustering algorithm">
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260 <option value="none">No clustering</option>
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261 <option value="kmeans">Kmeans clustering</option>
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262 </param>
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263 <when value="kmeans">
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264 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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265 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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266 </when>
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267 <when value="none" />
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268 </conditional>
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269 </when>
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270 <when value="yes" />
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271 </conditional>
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272 </xml>
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273
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274 <token name="@KMEANS_CLUSTERING@">
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275 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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276 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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277 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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278 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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279 #end if
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280 #end if
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281 #end if
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282 </token>
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283
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284 <xml name="samFlag">
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285 <param name="samFlag" type="integer" optional="true" value=""
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286 label="Filter reads based on the SAM flag"
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287 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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288 </xml>
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289 <xml name="plotNumbers">
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290 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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291 label="Plot the correlation value"
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292 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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293 </xml>
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294 <xml name="doNotExtendPairedEnds">
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295 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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296 label="Do not extend paired ends"
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297 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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298 </xml>
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299
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300 <xml name="ignoreDuplicates">
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301 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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302 label="Ignore duplicates"
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303 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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304 </xml>
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305
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306 <xml name="minMappingQuality">
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307 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
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308 label="Minimum mapping quality"
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309 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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310 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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311 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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312 </xml>
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313
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314 <xml name="skipZeros">
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315 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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316 label ="Skip zeros"
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317 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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318 </xml>
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319
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320 <xml name="fragmentLength">
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321 <param name="fragmentLength" type="integer" value="300" min="1"
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322 label="Fragment length used for the sequencing"
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323 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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324 </xml>
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325
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326 <xml name="scaleFactor">
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327 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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328 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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329 </xml>
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330
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331 <xml name="xMax">
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332 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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333 label="Max value for the x-axis in counts per bin" />
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334 </xml>
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335
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336 <xml name="filterThreshold">
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337 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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338 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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339
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340 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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341 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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342 </xml>
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343
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344
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345 <xml name="pseudocount">
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346 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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347 </xml>
5
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348 <xml name='matrix_h5_cooler_macro'>
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349 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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350 label="Matrix to compute on"/>
5
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351 </xml>
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352 <xml name='matrix_h5_cooler_multiple_macro'>
8
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353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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354 label="Matricies to compute on" multiple="true"/>
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355 </xml>
13
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356
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357
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358
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359 <xml name='convertFormat_single_macro'>
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360 <conditional name="inputFormat_conditional">
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361 <param name="inputFormat_selector" type="select" label="Choose input file type">
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362 <option value="optionCool" selected="True">cool</option>
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363 <option value="optionH5">h5</option>
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364 <option value="optionHic">hic</option>
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365 <option value="optionHomer">Homer</option>
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366 <option value="optionHicpro">HiCPro</option>
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367 </param>
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368 <when value="optionCool">
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369 <expand macro='matrix_h5_cooler_macro' />
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370 <param name='correctionName' type='text' label='Correction factors column name'/>
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371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
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372 <param name='chromosome' type='text' label='Load only one chromosome'/>
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373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
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374
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375 </when>
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376 <when value="optionH5">
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377 <expand macro='matrix_h5_cooler_macro' />
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378 </when>
14
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379 <when value="optionHic">
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380 <param name='matrixHic' type='data' format='hic' label='.hic matrix'/>
13
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381 <param name='resolutions' type='text' label='List of resolutions'/>
14
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382 </when>
13
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383
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384 <when value="optionHomer">
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385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix'/>
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386 </when>
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387
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388 <when value="optionHicpro">
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389 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix'/>
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390 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file'/>
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391 </when>
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392 </conditional>
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393 </xml>
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394
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395 <xml name='convertFormat_multiple_macro'>
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396 <conditional name="inputFormat_conditional">
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397 <param name="inputFormat_selector" type="select" label="Choose input file type">
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398 <option value="optionCool" selected="True">cool</option>
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399 <option value="optionH5">h5</option>
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400 <option value="optionHomer">Homer</option>
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401 <option value="optionHicpro">HiCPro</option>
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402 </param>
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403 <when value="optionCool">
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404 <expand macro='matrix_h5_cooler_multiple_macro' />
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405 <param name='correctionName' type='text' label='Correction factors column name'/>
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406 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
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407 <param name='chromosome' type='text' label='Load only one chromosome'/>
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408 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
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409
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410 </when>
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411 <when value="optionH5">
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412 <expand macro='matrix_h5_cooler_multiple_macro' />
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413 </when>
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414
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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415 <when value="optionHomer">
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416 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/>
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417 </when>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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418
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
419 <when value="optionHicpro">
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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420 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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421 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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422 </when>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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423 </conditional>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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424 </xml>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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425 <xml name='convertFormat_single_output_macro'>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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426 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
427
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
428 <conditional name="outputFormat_conditional">
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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429 <param name="outputFormat_selector" type="select" label="Choose output file type">
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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430 <option value="cool" selected="True">cool</option>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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431 <option value="h5">h5</option>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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432 <option value="homer">Homer</option>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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433 <option value="ginteractions">ginteractions</option>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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434
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
435 </param>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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436 <when value="cool">
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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437 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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438 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column'/>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
439 </when>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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440 <when value='h5'/>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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441 <when value='homer'/>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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442 <when value='ginteractions'/>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
443
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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444 </conditional>
40b33e101621 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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445 </xml>
0
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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446 <token name="@REFERENCES@">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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447
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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448 .. class:: infomark
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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449
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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450 For more information on the tools, please visit our `help site`_.
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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451
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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452 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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453
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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454 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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455
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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456 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2
2c0069f645bc planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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458 .. _help site: https://hicexplorer.readthedocs.org
0
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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459
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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460 </token>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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461
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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462
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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463 <xml name="multiple_input_bams">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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464 <repeat name="input_files" title="BAM files" min="2">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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465 <param name="bamfile" type="data" format="bam"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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466 label="Bam file"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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467 help="The BAM file must be sorted."/>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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468 <param name="label" type="text" size="30" optional="true" value=""
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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469 label="Label"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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470 help="Label to use in the output. If not given the dataset name will be used instead."/>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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471 </repeat>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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472 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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473
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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474 <xml name="multiple_input_bigwigs">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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475 <repeat name="input_files" title="BigWig files" min="2">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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476 <param name="bigwigfile" type="data" format="bigwig"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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477 label="Bigwig file"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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478 help="The Bigwig file must be sorted."/>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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479 <param name="label" type="text" size="30" optional="true" value=""
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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480 label="Label"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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481 help="Label to use in the output. If not given the dataset name will be used instead."/>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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482 </repeat>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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483 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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484
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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485 <xml name="plotTitle">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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486 <param name="plotTitle" type="text" value="" size="30" optional="True"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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487 label="Title of the plot"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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489 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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490
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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491 <token name="@multiple_input_bams@">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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492 #import tempfile
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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494 #set files=[]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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495 #set labels=[]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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496 #for $i in $input_files:
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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497 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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498 #set $temp_input_path = $temp_input_handle.name
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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499 #silent $temp_input_handle.close()
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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500 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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501 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
502 #silent $files.append('%s.bam' % $temp_input_path)
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
503
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
504 ##set $files += [str($i.bamfile)]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
505 #if str($i.label.value) != "":
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
506 #set $labels += ["\"%s\"" % ($i.label.value)]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
507 #else
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
508 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
509 #end if
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
510 #end for
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
511 </token>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
512
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
513 <token name="@multiple_input_bigwigs@">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
514 #import tempfile
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
515 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
516 #set files=[]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
517 #set labels=[]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
518 #for $i in $input_files:
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
519 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
520 #set $temp_input_path = $temp_input_handle.name
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
521 #silent $temp_input_handle.close()
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
522 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
523 #silent $files.append('%s.bw' % $temp_input_path)
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
524
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
525 ##set $files += [str($i.bigwigfile)]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
526 #if str($i.label.value) != "":
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
527 #set $labels += ["\"%s\"" % ($i.label.value)]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
528 #else
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
529 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
530 #end if
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
531 #end for
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
532 </token>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
533
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
534 <xml name="reference_genome_source">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
535 <conditional name="source">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
536 <param name="ref_source" type="select" label="Reference genome">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
537 <option value="cached">locally cached</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
538 <option value="history">in your history</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
539 </param>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
540 <when value="cached">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
541 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
542 <options from_data_table="deepTools_seqs">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
543 <filter type="sort_by" column="1" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
544 <validator type="no_options" message="No indexes are available." />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
545 </options>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
546 </param>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
547 </when>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
548 <when value="history">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
549 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
550 </when>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
551 </conditional>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
552 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
553
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
554 <token name="@reference_genome_source@">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
555 #if $source.ref_source=="history":
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
556 --genome $source.input1
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
557 #else:
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
558 --genome "${source.input1_2bit.fields.path}"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
559 #end if
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
560 </token>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
561
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
562 <xml name="effectiveGenomeSize">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
563 <conditional name="effectiveGenomeSize">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
564 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
565 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.
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
566 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
567 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.">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
568 <option value="93260000">ce10 (93260000)</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
569 <option value="121400000">dm3 (121400000)</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
570 <option value="2451960000" selected="true">hg19 (2451960000)</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
571 <option value="2150570000">mm9 (2150570000)</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
572 <option value="specific">user specified</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
573 </param>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
574 <when value="specific">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
575 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
576 </when>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
577 <when value="2150570000" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
578 <when value="2451960000" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
579 <when value="121400000" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
580 <when value="93260000" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
581 </conditional>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
582 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
583
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
584 <xml name="image_file_format">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
585 <param name="outFileFormat" type="select" label="Image file format">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
586 <option value="png" selected="true">png</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
587 <option value="pdf">pdf</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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588 <option value="svg">svg</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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589 <option value="eps">eps</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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590 <option value="emf">emf</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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591 </param>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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592 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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593
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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594 <xml name="missingDataAsZero">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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595 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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596 label ="Treat missing data as zero"
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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597 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." />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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598 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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599
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
600 <xml name="input_save_matrix_values">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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601 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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602 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
603
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
604 <xml name="input_graphic_output_settings">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
605 <conditional name="output" >
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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606 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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607 <option value="no" selected="true">no</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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608 <option value="yes">yes</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
609 </param>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
610 <when value="no" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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611 <when value="yes">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
612 <yield />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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613 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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614 <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."/>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
615 </when>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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616 </conditional>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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617 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
618
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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619 <xml name="input_image_file_format">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
620 <param name="outFileFormat" type="select" label="Image file format">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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621 <option value="png" selected="true">png</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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622 <option value="pdf">pdf</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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623 <option value="svg">svg</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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624 <option value="eps">eps</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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625 <option value="emf">emf</option>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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626 </param>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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627 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
628
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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629 <xml name="output_image_file_format">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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630 <data format="png" name="outFileName" label="${tool.name} image">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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631 <change_format>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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632 <when input="output.outFileFormat" value="pdf" format="pdf" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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633 <when input="output.outFileFormat" value="svg" format="svg" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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634 <when input="output.outFileFormat" value="eps" format="eps" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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635 <when input="output.outFileFormat" value="emf" format="emf" />
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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636 </change_format>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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637 </data>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
638 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
639
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
640 <xml name="output_save_matrix_values">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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641 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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642 <filter>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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643 ((
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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644 output['showOutputSettings'] == 'yes' and
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
645 output['saveMatrix'] is True
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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646 ))
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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647 </filter>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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648 </data>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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649 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
650
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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651 <xml name="output_graphic_outputs">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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652 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
653 <filter>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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654 ((
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
655 output['showOutputSettings'] == 'yes' and
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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656 output['saveData'] is True
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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657 ))
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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658 </filter>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
659 </data>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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660 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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661 <filter>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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662 ((
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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663 output['showOutputSettings'] == 'yes' and
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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664 output['saveSortedRegions'] is True
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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665 ))
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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666 </filter>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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667 </data>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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668 </xml>
a9050bffb50c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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669
2
2c0069f645bc planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
670 <xml name="track_input_h5_macro">
5
c3703afea1b1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
2
2c0069f645bc planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
672 </xml>
2c0069f645bc planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
673 <xml name="track_input_bed_macro">
2c0069f645bc planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
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675 </xml>
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676 <xml name="track_input_bedgraph_macro">
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677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
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678 </xml>
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679 <xml name="track_input_bigwig_macro">
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680 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
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681 </xml>
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682 <xml name="track_input_bedgraph_matrix_macro">
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683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
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684 </xml>
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685 <xml name="track_input_tabular_macro">
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686 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
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687 </xml>
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688 <xml name="plot_title">
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689 <param name="title" type="text" optional="true" label="Plot title"/>
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690 </xml>
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691
2
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692 <xml name="spacer_macro">
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693 <param name="spacer_width" type="float" value="" optional="True"
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694 label="Include spacer at the end of the track." help="Width of the spacer." />
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695 </xml>
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696 <xml name="fontsize_macro">
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697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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698 </xml>
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699 </macros>