annotate macros.xml @ 5:1923cc7e6bc2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
author iuc
date Fri, 11 Dec 2020 21:11:52 +0000
parents 41e1d7a40b3b
children b75f87deaa15
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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@">3.4.3</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 $use_range.range_min:$use_range.range_max
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7 #end if
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8 </token>
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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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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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64
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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>
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85 <option value="autumn">autumn</option>
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diff changeset
86 <option value="winter">winter</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
87 <option value="hot">hot</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
88 <option value="coolwarm">coolwarm</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
89 <option value="cool">cool</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
90 <option value="seismic">seismic</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
91 <option value="terrain">terrain</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
92 <option value="ocean">ocean</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
93 <option value="rainbow">rainbow</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
94 <option value="bone">bone</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
95 <option value="flag">flag</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
96 <option value="prism">prism</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
97 <option value="cubehelix">cubehelix</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
98 <option value="binary">binary</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
99 <option value="pink">pink</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
100 <option value="gray">gray</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
101 <option value="copper">copper</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
102 <option value="BrBG">BrBG</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
103 <option value="BuGn">BuGn</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
104 <option value="BuPu">BuPu</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
105 <option value="GnBu">GnBu</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
106 <option value="OrRd">OrRd</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
107 <option value="PiYG">PiYG</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
108 <option value="PRGn">PRGn</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
109 <option value="PuOr">PuOr</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
110 <option value="PuRd">PuRd</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
111 <option value="PuBu">PuBu</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
112 <option value="RdBu">RdBu</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
113 <option value="RdGy">RdGy</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
114 <option value="RdPu">RdPu</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
115 <option value="YlGn">YlGn</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
116 <option value="PuBuGn">PuBuGn</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
117 <option value="RdYlGn">RdYlGn</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
118 <option value="YlGnBu">YlGnBu</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
119 <option value="YlOrBr">YlOrBr</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
120 <option value="YlOrRd">YlOrRd</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
121 <option value="gist_gray">gist_gray</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
122 <option value="gist_stern">gist_stern</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
123 <option value="gist_earth">gist_earth</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
124 <option value="gist_yarg">gist_yarg</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
125 <option value="gist_ncar">gist_ncar</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
126 <option value="gist_rainbow">gist_rainbow</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
127 <option value="gist_heat">gist_heat</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
128 <option value="gnuplot">gnuplot</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
129 <option value="gnuplot2">gnuplot2</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
130 <option value="CMRmap">CMRmap</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
131 <option value="bwr">bwr</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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parents:
diff changeset
132 <option value="hsv">hsv</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
133 <option value="brg">brg</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
134 <option value="jet">jet</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
135 <option value="afmhot">afmhot</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
136 <option value="plasma">plasma</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
137 <option value="Accent_r">Accent reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
138 <option value="Spectral_r">Spectral reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
139 <option value="Set1_r">Set1 reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
140 <option value="Set2_r">Set2 reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
141 <option value="Set3_r">Set3 reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
142 <option value="Dark2_r">Dark2 reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
143 <option value="Reds_r">Reds reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
144 <option value="Oranges_r">Oranges reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
145 <option value="Greens_r">Greens reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
146 <option value="Blues_r">Blues reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
147 <option value="Greys_r">Greys reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
148 <option value="Purples_r">Purples reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
149 <option value="Paired_r">Paired reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
150 <option value="Pastel1_r">Pastel1 reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
151 <option value="Pastel2_r">Pastel2 reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
152 <option value="spring_r">spring reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
153 <option value="summer_r">summer reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
154 <option value="autumn_r">autumn reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
155 <option value="winter_r">winter reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
156 <option value="hot_r">hot reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
157 <option value="coolwarm_r">coolwarm reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
158 <option value="cool_r">cool reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
159 <option value="seismic_r">seismic reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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parents:
diff changeset
160 <option value="terrain_r">terrain reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
161 <option value="ocean_r">ocean reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
162 <option value="rainbow_r">rainbow reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
163 <option value="bone_r">bone reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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parents:
diff changeset
164 <option value="flag_r">flag reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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diff changeset
165 <option value="prism_r">prism reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
166 <option value="cubehelix_r">cubehelix reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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parents:
diff changeset
167 <option value="binary_r">binary reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
168 <option value="pink_r">pink reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
169 <option value="gray_r">gray reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents:
diff changeset
170 <option value="copper_r">copper reversed</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
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171 <option value="BrBG_r">BrBG reversed</option>
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172 <option value="BuGn_r">BuGn reversed</option>
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173 <option value="BuPu_r">BuPu reversed</option>
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174 <option value="GnBu_r">GnBu reversed</option>
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175 <option value="OrRd_r">OrRd reversed</option>
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176 <option value="PiYG_r">PiYG reversed</option>
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177 <option value="PRGn_r">PRGn reversed</option>
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178 <option value="PuOr_r">PuOr reversed</option>
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179 <option value="PuRd_r">PuRd reversed</option>
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180 <option value="PuBu_r">PuBu reversed</option>
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181 <option value="RdBu_r">RdBu reversed</option>
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182 <option value="RdGy_r">RdGy reversed</option>
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183 <option value="RdPu_r">RdPu reversed</option>
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184 <option value="YlGn_r">YlGn reversed</option>
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185 <option value="PuBuGn_r">PuBuGn reversed</option>
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186 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
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187 <option value="RdYlGn_r">RdYlGn reversed</option>
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188 <option value="YlGnBu_r">YlGnBu reversed</option>
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189 <option value="YlOrBr_r">YlOrBr reversed</option>
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190 <option value="YlOrRd_r">YlOrRd reversed</option>
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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>
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194 <option value="gist_yarg_r">gist_yarg reversed</option>
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195 <option value="gist_ncar_r">gist_ncar reversed</option>
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196 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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197 <option value="gist_heat_r">gist_heat reversed</option>
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198 <option value="gnuplot_r">gnuplot reversed</option>
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199 <option value="gnuplot2_r">gnuplot2 reversed</option>
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200 <option value="CMRmap_r">CMRmap reversed</option>
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201 <option value="bwr_r">bwr reversed</option>
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202 <option value="hsv_r">hsv reversed</option>
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203 <option value="brg_r">brg reversed</option>
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204 <option value="jet_r">jet reversed</option>
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205 <option value="afmhot_r">afmhot reversed</option>
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206 <option value="plasma_r">plasma reversed</option>
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207 </param>
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208 </xml>
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209
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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"
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213 label="Hi-C Matrix file"
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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>
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219 </xml>
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220
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221 <token name="@multiple_input_matrices@">
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222 #set $matrices = []
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223 #set $mlabels = []
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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, $i.matrix.ext))
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227
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228 #if str($i.mlabel.value) != "":
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229 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
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230 #else
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231 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
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232 #end if
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233 #end for
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234 #set $mlabels = ' '.join($mlabels)
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235 #set $matrices = ' '.join($matrices)
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236 </token>
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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>
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241
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242 <xml name="region">
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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>
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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>
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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"/>
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351 </xml>
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352 <xml name='matrix_h5_cooler_multiple_macro'>
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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>
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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>
1
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364 <option value="optionHic">hic</option>
0
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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>
1
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379 <when value="optionHic">
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380 <param name='matrixHic' type='data' format='hic' label='.hic matrix'/>
0
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381 <param name='resolutions' type='text' label='List of resolutions'/>
1
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382 </when>
0
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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
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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
450605e43e25 "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>
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418
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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419 <when value="optionHicpro">
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420 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/>
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421 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/>
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422 </when>
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423 </conditional>
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424 </xml>
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425 <xml name='convertFormat_single_output_macro'>
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426 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
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427
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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428 <conditional name="outputFormat_conditional">
450605e43e25 "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">
450605e43e25 "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>
450605e43e25 "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>
450605e43e25 "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>
450605e43e25 "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>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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434
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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435 </param>
450605e43e25 "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">
450605e43e25 "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'/>
450605e43e25 "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'/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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439 </when>
450605e43e25 "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'/>
450605e43e25 "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'/>
450605e43e25 "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'/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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443
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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444 </conditional>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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445 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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446 <token name="@REFERENCES@">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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447
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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448 .. class:: infomark
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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449
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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450 For more information on the tools, please visit our `help site`_.
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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451
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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453
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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`_.
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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455
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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456 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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458 .. _help site: https://hicexplorer.readthedocs.org
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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459
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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460 </token>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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461
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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462
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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463 <xml name="multiple_input_bams">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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464 <repeat name="input_files" title="BAM files" min="2">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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465 <param name="bamfile" type="data" format="bam"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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466 label="Bam file"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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467 help="The BAM file must be sorted."/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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468 <param name="label" type="text" size="30" optional="true" value=""
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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469 label="Label"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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470 help="Label to use in the output. If not given the dataset name will be used instead."/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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471 </repeat>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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472 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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473
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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474 <xml name="multiple_input_bigwigs">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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475 <repeat name="input_files" title="BigWig files" min="2">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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476 <param name="bigwigfile" type="data" format="bigwig"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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477 label="Bigwig file"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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478 help="The Bigwig file must be sorted."/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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479 <param name="label" type="text" size="30" optional="true" value=""
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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480 label="Label"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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481 help="Label to use in the output. If not given the dataset name will be used instead."/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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482 </repeat>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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483 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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484
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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485 <xml name="plotTitle">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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486 <param name="plotTitle" type="text" value="" size="30" optional="True"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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487 label="Title of the plot"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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489 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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490
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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491 <token name="@multiple_input_bams@">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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492 #import tempfile
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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494 #set files=[]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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495 #set labels=[]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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496 #for $i in $input_files:
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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497 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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498 #set $temp_input_path = $temp_input_handle.name
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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499 #silent $temp_input_handle.close()
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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500 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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501 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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502 #silent $files.append('%s.bam' % $temp_input_path)
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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503
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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504 ##set $files += [str($i.bamfile)]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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505 #if str($i.label.value) != "":
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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506 #set $labels += ["\"%s\"" % ($i.label.value)]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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507 #else
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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508 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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509 #end if
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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510 #end for
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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511 </token>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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512
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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513 <token name="@multiple_input_bigwigs@">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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514 #import tempfile
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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515 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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516 #set files=[]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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517 #set labels=[]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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518 #for $i in $input_files:
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519 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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520 #set $temp_input_path = $temp_input_handle.name
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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521 #silent $temp_input_handle.close()
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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522 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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523 #silent $files.append('%s.bw' % $temp_input_path)
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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524
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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525 ##set $files += [str($i.bigwigfile)]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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526 #if str($i.label.value) != "":
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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527 #set $labels += ["\"%s\"" % ($i.label.value)]
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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528 #else
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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529 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
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530 #end if
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531 #end for
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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532 </token>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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533
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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534 <xml name="reference_genome_source">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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535 <conditional name="source">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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536 <param name="ref_source" type="select" label="Reference genome">
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537 <option value="cached">locally cached</option>
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538 <option value="history">in your history</option>
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539 </param>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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540 <when value="cached">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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541 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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542 <options from_data_table="deepTools_seqs">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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543 <filter type="sort_by" column="1" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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544 <validator type="no_options" message="No indexes are available." />
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545 </options>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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546 </param>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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547 </when>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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548 <when value="history">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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549 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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550 </when>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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551 </conditional>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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552 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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553
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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554 <token name="@reference_genome_source@">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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555 #if $source.ref_source=="history":
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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556 --genome $source.input1
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557 #else:
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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558 --genome "${source.input1_2bit.fields.path}"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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559 #end if
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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560 </token>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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561
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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562 <xml name="effectiveGenomeSize">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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563 <conditional name="effectiveGenomeSize">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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564 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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.
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
566 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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.">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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568 <option value="93260000">ce10 (93260000)</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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569 <option value="121400000">dm3 (121400000)</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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570 <option value="2451960000" selected="true">hg19 (2451960000)</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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571 <option value="2150570000">mm9 (2150570000)</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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572 <option value="specific">user specified</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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573 </param>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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574 <when value="specific">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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575 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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576 </when>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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577 <when value="2150570000" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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578 <when value="2451960000" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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579 <when value="121400000" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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580 <when value="93260000" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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581 </conditional>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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582 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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583
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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584 <xml name="image_file_format">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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585 <param name="outFileFormat" type="select" label="Image file format">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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586 <option value="png" selected="true">png</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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587 <option value="pdf">pdf</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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588 <option value="svg">svg</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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589 <option value="eps">eps</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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590 <option value="emf">emf</option>
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591 </param>
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592 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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593
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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594 <xml name="missingDataAsZero">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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595 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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596 label ="Treat missing data as zero"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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." />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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598 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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599
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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600 <xml name="input_save_matrix_values">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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601 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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602 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
603
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
604 <xml name="input_graphic_output_settings">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
605 <conditional name="output" >
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
606 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
607 <option value="no" selected="true">no</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
608 <option value="yes">yes</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
609 </param>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
610 <when value="no" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
611 <when value="yes">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
612 <yield />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
613 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
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."/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
615 </when>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
616 </conditional>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
617 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
618
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
619 <xml name="input_image_file_format">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
620 <param name="outFileFormat" type="select" label="Image file format">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
621 <option value="png" selected="true">png</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
622 <option value="pdf">pdf</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
623 <option value="svg">svg</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
624 <option value="eps">eps</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
625 <option value="emf">emf</option>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
626 </param>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
627 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
628
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
629 <xml name="output_image_file_format">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
630 <data format="png" name="outFileName" label="${tool.name} image">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
631 <change_format>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
632 <when input="output.outFileFormat" value="pdf" format="pdf" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
633 <when input="output.outFileFormat" value="svg" format="svg" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
634 <when input="output.outFileFormat" value="eps" format="eps" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
635 <when input="output.outFileFormat" value="emf" format="emf" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
636 </change_format>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
637 </data>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
638 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
639
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
640 <xml name="output_save_matrix_values">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
641 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
642 <filter>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
643 ((
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
644 output['showOutputSettings'] == 'yes' and
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
645 output['saveMatrix'] is True
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
646 ))
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
647 </filter>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
648 </data>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
649 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
650
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
651 <xml name="output_graphic_outputs">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
652 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
653 <filter>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
654 ((
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
655 output['showOutputSettings'] == 'yes' and
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
656 output['saveData'] is True
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
657 ))
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
658 </filter>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
659 </data>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
660 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
661 <filter>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
662 ((
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
663 output['showOutputSettings'] == 'yes' and
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
664 output['saveSortedRegions'] is True
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
665 ))
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
666 </filter>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
667 </data>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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668 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
669
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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670 <xml name="track_input_h5_macro">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
672 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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673 <xml name="track_input_bed_macro">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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675 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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676 <xml name="track_input_bedgraph_macro">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
678 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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679 <xml name="track_input_bigwig_macro">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
680 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
681 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
682 <xml name="track_input_bedgraph_matrix_macro">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
684 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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685 <xml name="track_input_tabular_macro">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
686 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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687 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
688 <xml name="plot_title">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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689 <param name="title" type="text" optional="true" label="Plot title"/>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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690 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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691
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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692 <xml name="spacer_macro">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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693 <param name="spacer_width" type="float" value="" optional="True"
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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694 label="Include spacer at the end of the track." help="Width of the spacer." />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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695 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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696 <xml name="fontsize_macro">
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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698 </xml>
450605e43e25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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699 </macros>