annotate macros.xml @ 18:5443b2b1165f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
author iuc
date Fri, 11 Dec 2020 21:01:31 +0000
parents bc027a1c0952
children e4cb7809df61
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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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9
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
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13 <yield />
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14 </requirements>
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15 <version_command>@BINARY@ --version</version_command>
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16 </xml>
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18 <token name="@CHROMOSOME_LIST@">
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19 #if $chromosome_list:
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20 #set $chromosomes = []
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21 #for $chrom in $chromosome_list:
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22 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
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23 #end for
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24 #set $chromosome_string = ' '.join($chromosomes)
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25 --chromosomes $chromosome_string
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26 #end if
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27 </token>
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29 <xml name="chromosome_list">
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30 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
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31 <param argument="--chromosomes" type="text" value="" >
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32 <validator type="empty_field" />
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33 </param>
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34 </repeat>
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35 </xml>
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36
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37 <xml name="citations">
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38 <citations>
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39 <citation type="doi">10.5281/zenodo.1133705</citation>
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40 <yield />
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41 </citations>
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42 </xml>
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44 <xml name="zMax">
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45 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
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46 </xml>
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47 <xml name="use_range">
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48 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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49 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
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50 <option value="no_use_range">No restriction</option>
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51 <option value="yes_use_range">Only consider counts within a range</option>
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52 </param>
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53 <when value="no_use_range"/>
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54 <when value="yes_use_range">
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55 <expand macro='range' />
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56 </when>
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57 </conditional>
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58 </xml>
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59
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60 <xml name="range">
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61 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
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62 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
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63 </xml>
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65 <xml name="colormap">
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66 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
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67 <option value="RdYlBu">RdYlBu</option>
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68 <option value="Accent">Accent</option>
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69 <option value="Spectral">Spectral</option>
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70 <option value="Set1">Set1</option>
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71 <option value="Set2">Set2</option>
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72 <option value="Set3">Set3</option>
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73 <option value="Dark2">Dark2</option>
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74 <option value="Reds">Reds</option>
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75 <option value="Oranges">Oranges</option>
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76 <option value="Greens">Greens</option>
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77 <option value="Blues">Blues</option>
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78 <option value="Greys">Greys</option>
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79 <option value="Purples">Purples</option>
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80 <option value="Paired">Paired</option>
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81 <option value="Pastel1">Pastel1</option>
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82 <option value="Pastel2">Pastel2</option>
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83 <option value="spring">spring</option>
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84 <option value="summer">summer</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
85 <option value="autumn">autumn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
86 <option value="winter">winter</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
87 <option value="hot">hot</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
88 <option value="coolwarm">coolwarm</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
89 <option value="cool">cool</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
90 <option value="seismic">seismic</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
91 <option value="terrain">terrain</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
92 <option value="ocean">ocean</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
93 <option value="rainbow">rainbow</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
94 <option value="bone">bone</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
95 <option value="flag">flag</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
96 <option value="prism">prism</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
97 <option value="cubehelix">cubehelix</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
98 <option value="binary">binary</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
99 <option value="pink">pink</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
100 <option value="gray">gray</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
101 <option value="copper">copper</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
102 <option value="BrBG">BrBG</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
103 <option value="BuGn">BuGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
104 <option value="BuPu">BuPu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
105 <option value="GnBu">GnBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
106 <option value="OrRd">OrRd</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
107 <option value="PiYG">PiYG</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
108 <option value="PRGn">PRGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
109 <option value="PuOr">PuOr</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
110 <option value="PuRd">PuRd</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
111 <option value="PuBu">PuBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
112 <option value="RdBu">RdBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
113 <option value="RdGy">RdGy</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
114 <option value="RdPu">RdPu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
115 <option value="YlGn">YlGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
116 <option value="PuBuGn">PuBuGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
117 <option value="RdYlGn">RdYlGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
118 <option value="YlGnBu">YlGnBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
119 <option value="YlOrBr">YlOrBr</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
120 <option value="YlOrRd">YlOrRd</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
121 <option value="gist_gray">gist_gray</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
122 <option value="gist_stern">gist_stern</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
123 <option value="gist_earth">gist_earth</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
124 <option value="gist_yarg">gist_yarg</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
125 <option value="gist_ncar">gist_ncar</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
126 <option value="gist_rainbow">gist_rainbow</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
127 <option value="gist_heat">gist_heat</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
128 <option value="gnuplot">gnuplot</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
129 <option value="gnuplot2">gnuplot2</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
130 <option value="CMRmap">CMRmap</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
131 <option value="bwr">bwr</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
132 <option value="hsv">hsv</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
133 <option value="brg">brg</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
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134 <option value="jet">jet</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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135 <option value="afmhot">afmhot</option>
13
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
136 <option value="plasma">plasma</option>
0
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
137 <option value="Accent_r">Accent reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
138 <option value="Spectral_r">Spectral reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
139 <option value="Set1_r">Set1 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
140 <option value="Set2_r">Set2 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
141 <option value="Set3_r">Set3 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
142 <option value="Dark2_r">Dark2 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
143 <option value="Reds_r">Reds reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
144 <option value="Oranges_r">Oranges reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
145 <option value="Greens_r">Greens reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
146 <option value="Blues_r">Blues reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
147 <option value="Greys_r">Greys reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
148 <option value="Purples_r">Purples reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
149 <option value="Paired_r">Paired reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
150 <option value="Pastel1_r">Pastel1 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
151 <option value="Pastel2_r">Pastel2 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
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152 <option value="spring_r">spring reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
153 <option value="summer_r">summer reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
154 <option value="autumn_r">autumn reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
155 <option value="winter_r">winter reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
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156 <option value="hot_r">hot reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
157 <option value="coolwarm_r">coolwarm reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
158 <option value="cool_r">cool reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
159 <option value="seismic_r">seismic reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
160 <option value="terrain_r">terrain reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
161 <option value="ocean_r">ocean reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
162 <option value="rainbow_r">rainbow reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
163 <option value="bone_r">bone reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
164 <option value="flag_r">flag reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
165 <option value="prism_r">prism reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
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166 <option value="cubehelix_r">cubehelix reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
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167 <option value="binary_r">binary reversed</option>
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168 <option value="pink_r">pink reversed</option>
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169 <option value="gray_r">gray reversed</option>
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170 <option value="copper_r">copper reversed</option>
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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>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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187 <option value="RdYlGn_r">RdYlGn reversed</option>
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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>
0
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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"
0
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214 help=""/>
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215 <param name="mlabel" type="text" size="30" optional="true" value=""
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216 label="Label"
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217 help="Label to use in the output. If not given the dataset name will be used instead."/>
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218 </repeat>
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219 </xml>
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220
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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221 <token name="@multiple_input_matrices@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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($file.element_identifier))]]></token>
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diff changeset
239 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
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240 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
0
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241
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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>
5
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348 <xml name='matrix_h5_cooler_macro'>
8
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349 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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350 label="Matrix to compute on"/>
5
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351 </xml>
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352 <xml name='matrix_h5_cooler_multiple_macro'>
8
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353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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354 label="Matricies to compute on" multiple="true"/>
5
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355 </xml>
13
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356
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357
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358
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359 <xml name='convertFormat_single_macro'>
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360 <conditional name="inputFormat_conditional">
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361 <param name="inputFormat_selector" type="select" label="Choose input file type">
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362 <option value="optionCool" selected="True">cool</option>
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363 <option value="optionH5">h5</option>
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364 <option value="optionHic">hic</option>
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365 <option value="optionHomer">Homer</option>
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366 <option value="optionHicpro">HiCPro</option>
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367 </param>
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368 <when value="optionCool">
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369 <expand macro='matrix_h5_cooler_macro' />
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370 <param name='correctionName' type='text' label='Correction factors column name'/>
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371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
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372 <param name='chromosome' type='text' label='Load only one chromosome'/>
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373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
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374
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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375 </when>
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376 <when value="optionH5">
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377 <expand macro='matrix_h5_cooler_macro' />
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378 </when>
14
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379 <when value="optionHic">
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380 <param name='matrixHic' type='data' format='hic' label='.hic matrix'/>
13
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381 <param name='resolutions' type='text' label='List of resolutions'/>
14
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382 </when>
13
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383
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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
9949f055db84 "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
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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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
9949f055db84 "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>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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418
9949f055db84 "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">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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420 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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421 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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422 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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423 </conditional>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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424 </xml>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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425 <xml name='convertFormat_single_output_macro'>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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426 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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427
9949f055db84 "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">
9949f055db84 "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">
9949f055db84 "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>
9949f055db84 "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>
9949f055db84 "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>
9949f055db84 "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>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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434
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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435 </param>
9949f055db84 "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">
9949f055db84 "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'/>
9949f055db84 "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'/>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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439 </when>
9949f055db84 "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'/>
9949f055db84 "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'/>
9949f055db84 "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'/>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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443
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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444 </conditional>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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445 </xml>
0
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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446 <token name="@REFERENCES@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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447
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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448 .. class:: infomark
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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449
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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450 For more information on the tools, please visit our `help site`_.
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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451
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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452 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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453
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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454 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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455
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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456 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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458 .. _help site: https://hicexplorer.readthedocs.org
0
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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459
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
460 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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461
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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462
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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463 <xml name="multiple_input_bams">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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464 <repeat name="input_files" title="BAM files" min="2">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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465 <param name="bamfile" type="data" format="bam"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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466 label="Bam file"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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467 help="The BAM file must be sorted."/>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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468 <param name="label" type="text" size="30" optional="true" value=""
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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469 label="Label"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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470 help="Label to use in the output. If not given the dataset name will be used instead."/>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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471 </repeat>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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472 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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473
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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474 <xml name="multiple_input_bigwigs">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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475 <repeat name="input_files" title="BigWig files" min="2">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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476 <param name="bigwigfile" type="data" format="bigwig"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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477 label="Bigwig file"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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478 help="The Bigwig file must be sorted."/>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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479 <param name="label" type="text" size="30" optional="true" value=""
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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480 label="Label"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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481 help="Label to use in the output. If not given the dataset name will be used instead."/>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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482 </repeat>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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483 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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484
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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485 <xml name="plotTitle">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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486 <param name="plotTitle" type="text" value="" size="30" optional="True"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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487 label="Title of the plot"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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489 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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490
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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491 <token name="@multiple_input_bams@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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492 #import tempfile
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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494 #set files=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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495 #set labels=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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496 #for $i in $input_files:
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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497 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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498 #set $temp_input_path = $temp_input_handle.name
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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499 #silent $temp_input_handle.close()
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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500 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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501 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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502 #silent $files.append('%s.bam' % $temp_input_path)
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
503
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
504 ##set $files += [str($i.bamfile)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
505 #if str($i.label.value) != "":
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
506 #set $labels += ["\"%s\"" % ($i.label.value)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
507 #else
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
508 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
509 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
510 #end for
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
511 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
512
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
513 <token name="@multiple_input_bigwigs@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
514 #import tempfile
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
515 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
516 #set files=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
517 #set labels=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
518 #for $i in $input_files:
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
519 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
520 #set $temp_input_path = $temp_input_handle.name
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
521 #silent $temp_input_handle.close()
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
522 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
523 #silent $files.append('%s.bw' % $temp_input_path)
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
524
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
525 ##set $files += [str($i.bigwigfile)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
526 #if str($i.label.value) != "":
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
527 #set $labels += ["\"%s\"" % ($i.label.value)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
528 #else
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
529 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
530 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
531 #end for
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
532 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
533
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
534 <xml name="reference_genome_source">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
535 <conditional name="source">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
536 <param name="ref_source" type="select" label="Reference genome">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
537 <option value="cached">locally cached</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
538 <option value="history">in your history</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
539 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
540 <when value="cached">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
541 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
542 <options from_data_table="deepTools_seqs">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
543 <filter type="sort_by" column="1" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
544 <validator type="no_options" message="No indexes are available." />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
545 </options>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
546 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
547 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
548 <when value="history">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
549 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
550 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
551 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
552 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
553
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
554 <token name="@reference_genome_source@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
555 #if $source.ref_source=="history":
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
556 --genome $source.input1
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
557 #else:
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
558 --genome "${source.input1_2bit.fields.path}"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
559 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
560 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
561
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
562 <xml name="effectiveGenomeSize">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
563 <conditional name="effectiveGenomeSize">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
564 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
565 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
566 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
567 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
568 <option value="93260000">ce10 (93260000)</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
569 <option value="121400000">dm3 (121400000)</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
570 <option value="2451960000" selected="true">hg19 (2451960000)</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
571 <option value="2150570000">mm9 (2150570000)</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
572 <option value="specific">user specified</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
573 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
574 <when value="specific">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
575 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
576 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
577 <when value="2150570000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
578 <when value="2451960000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
579 <when value="121400000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
580 <when value="93260000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
581 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
582 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
583
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
584 <xml name="image_file_format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
585 <param name="outFileFormat" type="select" label="Image file format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
586 <option value="png" selected="true">png</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
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587 <option value="pdf">pdf</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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588 <option value="svg">svg</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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589 <option value="eps">eps</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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590 <option value="emf">emf</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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591 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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592 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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593
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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594 <xml name="missingDataAsZero">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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595 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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596 label ="Treat missing data as zero"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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597 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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598 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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599
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
600 <xml name="input_save_matrix_values">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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601 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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602 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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603
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
604 <xml name="input_graphic_output_settings">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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605 <conditional name="output" >
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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606 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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607 <option value="no" selected="true">no</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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608 <option value="yes">yes</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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609 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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610 <when value="no" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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611 <when value="yes">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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612 <yield />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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613 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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614 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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615 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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616 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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617 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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618
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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619 <xml name="input_image_file_format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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620 <param name="outFileFormat" type="select" label="Image file format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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621 <option value="png" selected="true">png</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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622 <option value="pdf">pdf</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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623 <option value="svg">svg</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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624 <option value="eps">eps</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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625 <option value="emf">emf</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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626 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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627 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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628
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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629 <xml name="output_image_file_format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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630 <data format="png" name="outFileName" label="${tool.name} image">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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631 <change_format>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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632 <when input="output.outFileFormat" value="pdf" format="pdf" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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633 <when input="output.outFileFormat" value="svg" format="svg" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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634 <when input="output.outFileFormat" value="eps" format="eps" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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635 <when input="output.outFileFormat" value="emf" format="emf" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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636 </change_format>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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637 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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638 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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639
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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640 <xml name="output_save_matrix_values">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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641 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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642 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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643 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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644 output['showOutputSettings'] == 'yes' and
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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645 output['saveMatrix'] is True
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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646 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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647 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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648 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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649 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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650
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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651 <xml name="output_graphic_outputs">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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652 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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653 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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654 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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655 output['showOutputSettings'] == 'yes' and
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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656 output['saveData'] is True
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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657 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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658 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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659 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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660 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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661 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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662 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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663 output['showOutputSettings'] == 'yes' and
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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664 output['saveSortedRegions'] is True
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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665 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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666 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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667 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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668 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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669
2
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
670 <xml name="track_input_h5_macro">
5
44919af9194b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
2
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
672 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
673 <xml name="track_input_bed_macro">
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
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675 </xml>
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676 <xml name="track_input_bedgraph_macro">
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677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
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678 </xml>
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679 <xml name="track_input_bigwig_macro">
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680 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
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681 </xml>
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682 <xml name="track_input_bedgraph_matrix_macro">
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683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
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684 </xml>
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685 <xml name="track_input_tabular_macro">
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686 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
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687 </xml>
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688 <xml name="plot_title">
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689 <param name="title" type="text" optional="true" label="Plot title"/>
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690 </xml>
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691
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692 <xml name="spacer_macro">
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693 <param name="spacer_width" type="float" value="" optional="True"
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694 label="Include spacer at the end of the track." help="Width of the spacer." />
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695 </xml>
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696 <xml name="fontsize_macro">
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697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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698 </xml>
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699 </macros>