Mercurial > repos > bgruening > hicexplorer_hicfindtads

annotate macros.xml @ 20:ec4b948dc6f0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 12:47:13 +0000
parents 5746d61f0a91
children 755df866ad0c
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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="@TOOL_VERSION@">3.7.2</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@USE_RANGE@">
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6 #if $use_range.select_use_range == "yes_use_range":
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7 --range $use_range.range_min:$use_range.range_max
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8 #end if
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9 </token>
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement>
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14 <yield />
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15 </requirements>
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16 <version_command>@BINARY@ --version</version_command>
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17 </xml>
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19 <token name="@CHROMOSOME_LIST@">
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20 #if $chromosome_list:
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21 #set $chromosomes = []
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22 #for $chrom in $chromosome_list:
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23 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
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24 #end for
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25 #set $chromosome_string = ' '.join($chromosomes)
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26 --chromosomes $chromosome_string
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27 #end if
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28 </token>
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30 <xml name="chromosome_list">
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31 <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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32 <param argument="--chromosomes" type="text" value="">
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33 <validator type="empty_field" />
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34 </param>
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35 </repeat>
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36 </xml>
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37
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38 <xml name="citations">
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39 <citations>
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40 <citation type="doi">10.1093/nar/gkaa220</citation>
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41 <citation type="doi">10.1093/nar/gky504</citation>
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42 <yield />
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43 </citations>
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44 </xml>
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45 <xml name="dpi">
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46 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
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47 </xml>
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48
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49 <xml name="restrictionCutFile">
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50 <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
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51 (i.e. the region between one restriction site and the next)." />
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52 </xml>
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53
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54 <xml name="restrictionSequence">
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55 <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
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56 &quot;dangling-ends&quot;. If not given, such statistics will not be available.">
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57 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
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58 </param>
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59 </xml>
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60 <xml name="danglingSequence">
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61 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
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62 Each restriction enzyme recognizes a different DNA sequence and,
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63 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
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64 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
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65 For DpnII, the restriction site and dangling end sequence are the same: GATC.
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66 This information is easily found on the description of the restriction enzyme.
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67 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
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68 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
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69 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
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70 </param>
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71 </xml>
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73 <xml name="zMax">
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74 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />
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75 <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
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76 </xml>
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77 <xml name="use_range">
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78 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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79 <param name="select_use_range" argument="--range" type="select" label="Range restriction (in bp)" help="If given, only counts within the specified range are considered.">
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80 <option value="no_use_range">No restriction</option>
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81 <option value="yes_use_range">Only consider counts within a range</option>
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82 </param>
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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83 <when value="no_use_range" />
7
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84 <when value="yes_use_range">
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85 <expand macro='range' />
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86 </when>
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87 </conditional>
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88 </xml>
43332e51a712 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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89
43332e51a712 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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90 <xml name="range">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
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91 <param name='range_min' type="integer" value="" min="0" label="Minimum range to consider interactions" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions." />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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92 <param name='range_max' type="integer" value="" min="0" label="Maximum range to consider interactions" />
7
43332e51a712 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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93 </xml>
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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94
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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95 <xml name="colormap">
4
8b60271e7e54 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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96 <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">
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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97 <option value="RdYlBu">RdYlBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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98 <option value="Accent">Accent</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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99 <option value="Spectral">Spectral</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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100 <option value="Set1">Set1</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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101 <option value="Set2">Set2</option>
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102 <option value="Set3">Set3</option>
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103 <option value="Dark2">Dark2</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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104 <option value="Reds">Reds</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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105 <option value="Oranges">Oranges</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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106 <option value="Greens">Greens</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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107 <option value="Blues">Blues</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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108 <option value="Greys">Greys</option>
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109 <option value="Purples">Purples</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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110 <option value="Paired">Paired</option>
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111 <option value="Pastel1">Pastel1</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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112 <option value="Pastel2">Pastel2</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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113 <option value="spring">spring</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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114 <option value="summer">summer</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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115 <option value="autumn">autumn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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116 <option value="winter">winter</option>
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117 <option value="hot">hot</option>
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118 <option value="coolwarm">coolwarm</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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119 <option value="cool">cool</option>
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120 <option value="seismic">seismic</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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121 <option value="terrain">terrain</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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122 <option value="ocean">ocean</option>
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123 <option value="rainbow">rainbow</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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124 <option value="bone">bone</option>
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125 <option value="flag">flag</option>
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126 <option value="prism">prism</option>
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127 <option value="cubehelix">cubehelix</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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128 <option value="binary">binary</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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129 <option value="pink">pink</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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130 <option value="gray">gray</option>
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131 <option value="copper">copper</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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132 <option value="BrBG">BrBG</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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133 <option value="BuGn">BuGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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134 <option value="BuPu">BuPu</option>
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135 <option value="GnBu">GnBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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136 <option value="OrRd">OrRd</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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137 <option value="PiYG">PiYG</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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138 <option value="PRGn">PRGn</option>
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139 <option value="PuOr">PuOr</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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140 <option value="PuRd">PuRd</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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141 <option value="PuBu">PuBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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142 <option value="RdBu">RdBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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143 <option value="RdGy">RdGy</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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144 <option value="RdPu">RdPu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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145 <option value="YlGn">YlGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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146 <option value="PuBuGn">PuBuGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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147 <option value="RdYlGn">RdYlGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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148 <option value="YlGnBu">YlGnBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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149 <option value="YlOrBr">YlOrBr</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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150 <option value="YlOrRd">YlOrRd</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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151 <option value="gist_gray">gist_gray</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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152 <option value="gist_stern">gist_stern</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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153 <option value="gist_earth">gist_earth</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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154 <option value="gist_yarg">gist_yarg</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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155 <option value="gist_ncar">gist_ncar</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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156 <option value="gist_rainbow">gist_rainbow</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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157 <option value="gist_heat">gist_heat</option>
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158 <option value="gnuplot">gnuplot</option>
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159 <option value="gnuplot2">gnuplot2</option>
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160 <option value="CMRmap">CMRmap</option>
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161 <option value="bwr">bwr</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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162 <option value="hsv">hsv</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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163 <option value="brg">brg</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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164 <option value="jet">jet</option>
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165 <option value="afmhot">afmhot</option>
12
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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166 <option value="plasma">plasma</option>
0
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167 <option value="Accent_r">Accent reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
168 <option value="Spectral_r">Spectral reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
169 <option value="Set1_r">Set1 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
170 <option value="Set2_r">Set2 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
171 <option value="Set3_r">Set3 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
172 <option value="Dark2_r">Dark2 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
173 <option value="Reds_r">Reds reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
174 <option value="Oranges_r">Oranges reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
175 <option value="Greens_r">Greens reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
176 <option value="Blues_r">Blues reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
177 <option value="Greys_r">Greys reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
178 <option value="Purples_r">Purples reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
179 <option value="Paired_r">Paired reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
180 <option value="Pastel1_r">Pastel1 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
181 <option value="Pastel2_r">Pastel2 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
182 <option value="spring_r">spring reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
183 <option value="summer_r">summer reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
184 <option value="autumn_r">autumn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
185 <option value="winter_r">winter reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
186 <option value="hot_r">hot reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
187 <option value="coolwarm_r">coolwarm reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
188 <option value="cool_r">cool reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
189 <option value="seismic_r">seismic reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
190 <option value="terrain_r">terrain reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
191 <option value="ocean_r">ocean reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
192 <option value="rainbow_r">rainbow reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
193 <option value="bone_r">bone reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
194 <option value="flag_r">flag reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
195 <option value="prism_r">prism reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
196 <option value="cubehelix_r">cubehelix reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
197 <option value="binary_r">binary reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
198 <option value="pink_r">pink reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
199 <option value="gray_r">gray reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
200 <option value="copper_r">copper reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
201 <option value="BrBG_r">BrBG reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
202 <option value="BuGn_r">BuGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
203 <option value="BuPu_r">BuPu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
204 <option value="GnBu_r">GnBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
205 <option value="OrRd_r">OrRd reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
206 <option value="PiYG_r">PiYG reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
207 <option value="PRGn_r">PRGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
208 <option value="PuOr_r">PuOr reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
209 <option value="PuRd_r">PuRd reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
210 <option value="PuBu_r">PuBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
211 <option value="RdBu_r">RdBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
212 <option value="RdGy_r">RdGy reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
213 <option value="RdPu_r">RdPu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
214 <option value="YlGn_r">YlGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
215 <option value="PuBuGn_r">PuBuGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
216 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
217 <option value="RdYlGn_r">RdYlGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
218 <option value="YlGnBu_r">YlGnBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
219 <option value="YlOrBr_r">YlOrBr reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
220 <option value="YlOrRd_r">YlOrRd reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
221 <option value="gist_gray_r">gist_gray reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
222 <option value="gist_stern_r">gist_stern reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
223 <option value="gist_earth_r">gist_earth reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
224 <option value="gist_yarg_r">gist_yarg reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
225 <option value="gist_ncar_r">gist_ncar reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
226 <option value="gist_rainbow_r">gist_rainbow reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
227 <option value="gist_heat_r">gist_heat reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
228 <option value="gnuplot_r">gnuplot reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
229 <option value="gnuplot2_r">gnuplot2 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
230 <option value="CMRmap_r">CMRmap reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
231 <option value="bwr_r">bwr reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
232 <option value="hsv_r">hsv reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
233 <option value="brg_r">brg reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
234 <option value="jet_r">jet reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
235 <option value="afmhot_r">afmhot reversed</option>
12
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 10
diff changeset
236 <option value="plasma_r">plasma reversed</option>
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
237 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
238 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
239
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
240 <xml name="multiple_input_matrices">
8
b05f292d220c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 7
diff changeset
241 <repeat name="input_files" title="Hi-C Matrix files" min="2">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
242 <param name="matrix" type="data" format="h5,cool" label="Hi-C Matrix file" help="" />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
243 <param name="mlabel" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
244 </repeat>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
245 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
246
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
247 <token name="@multiple_input_matrices@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
248 #set $matrices = []
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
249 #set $mlabels = []
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
250 #for $counter, $i in enumerate($input_files):
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251 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
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252 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
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253
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254 #if str($i.mlabel.value) != "":
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255 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
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256 #else
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257 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
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258 #end if
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259 #end for
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260 #set $mlabels = ' '.join($mlabels)
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261 #set $matrices = ' '.join($matrices)
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262 </token>
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263
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264 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
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265 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
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266 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
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267
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268 <xml name="region">
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269 <param argument="--region" type="text" label="Region of the genome to limit the operation" help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500">
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270 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
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271 </param>
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272 </xml>
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273
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274 <xml name="kmeans_clustering">
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275 <conditional name="used_multiple_regions">
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276 <param name="used_multiple_regions_options" type="select" label="Did you compute the matrix with more than one groups of regions?" 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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277 <option value="yes">Yes, I used multiple groups of regions</option>
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278 <option value="no">No, I used only one group</option>
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279 </param>
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280 <when value="no">
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281 <conditional name="clustering">
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282 <param name="clustering_options" type="select" label="Clustering algorithm">
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283 <option value="none">No clustering</option>
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284 <option value="kmeans">Kmeans clustering</option>
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285 </param>
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286 <when value="kmeans">
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287 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 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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288 </when>
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289 <when value="none" />
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290 </conditional>
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291 </when>
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292 <when value="yes" />
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293 </conditional>
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294 </xml>
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295
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296 <token name="@KMEANS_CLUSTERING@">
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297 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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298 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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299 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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300 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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301 #end if
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302 #end if
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303 #end if
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304 </token>
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305
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306 <xml name="samFlag">
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307 <param name="samFlag" type="integer" optional="true" value="" label="Filter reads based on the SAM flag" 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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308 </xml>
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309 <xml name="plotNumbers">
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310 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" label="Plot the correlation value" help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)" />
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311 </xml>
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312 <xml name="doNotExtendPairedEnds">
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313 <param argument="--doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" label="Do not extend paired ends" 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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314 </xml>
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315 <xml name="ignoreDuplicates">
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316 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" label="Ignore duplicates" 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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317 </xml>
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318 <xml name="minMappingQuality">
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319 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" label="Minimum mapping quality" help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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320 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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321 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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322 </xml>
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323
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324 <xml name="skipZeros">
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325 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label="Skip zeros" 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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326 </xml>
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327
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328 <xml name="fragmentLength">
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329 <param argument="--fragmentLength" type="integer" value="300" min="1" label="Fragment length used for the sequencing" help="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)" />
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330 </xml>
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331
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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332 <xml name="scaleFactor">
18
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333 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)" />
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334 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
0
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335 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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336 <xml name="xMax">
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337 <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
0
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338 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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339 <xml name="filterThreshold">
18
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340 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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341 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect." />
0
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342 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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343 <xml name="pseudocount">
18
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344 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero." />
0
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345 </xml>
5
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346 <xml name='matrix_h5_cooler_macro'>
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347 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" />
5
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348 </xml>
db2cc9e1ff76 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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349 <xml name='matrix_h5_cooler_multiple_macro'>
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350 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
5
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351 </xml>
20
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parents: 19
diff changeset
352
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
diff changeset
353 <xml name='matrix_cooler_multiple_macro'>
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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354 <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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355 </xml>
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356 <xml name='convertFormat_single_macro'>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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357 <conditional name="inputFormat_conditional">
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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358 <param name="inputFormat_selector" type="select" label="Choose input file type">
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359 <option value="optionCool" selected="True">cool</option>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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360 <option value="optionH5">h5</option>
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361 <option value="optionHic">hic</option>
12
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362 <option value="optionHomer">Homer</option>
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363 <option value="optionHicpro">HiCPro</option>
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parents: 19
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364 <option value="option2Dtext">2D-text</option>
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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365
12
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366 </param>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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367 <when value="optionCool">
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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368 <expand macro='matrix_h5_cooler_macro' />
18
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parents: 17
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369 <param name='correctionName' type='text' label='Correction factors column name' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 17
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370 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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371 <param name='chromosome' type='text' label='Load only one chromosome' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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372 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
12
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373 </when>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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374 <when value="optionH5">
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diff changeset
375 <expand macro='matrix_h5_cooler_macro' />
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
376 </when>
13
d3fad161b318 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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377 <when value="optionHic">
18
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parents: 17
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378 <param name='matrixHic' type='data' format='hic' label='.hic matrix' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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379 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
380 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 17
diff changeset
381 </param>
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 17
diff changeset
382 </when>
12
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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383 <when value="optionHomer">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 17
diff changeset
384 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
12
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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385 </when>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
386 <when value="optionHicpro">
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parents: 19
diff changeset
387 <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
388 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
12
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
389 </when>
20
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
diff changeset
390 <when value="option2Dtext">
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 19
diff changeset
391 <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 19
diff changeset
392
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
diff changeset
393 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
diff changeset
394 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
diff changeset
395 </param>
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 19
diff changeset
396 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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397 </when>
12
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398 </conditional>
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399 </xml>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
400
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
401 <xml name='convertFormat_multiple_macro'>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
402 <conditional name="inputFormat_conditional">
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
403 <param name="inputFormat_selector" type="select" label="Choose input file type">
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
404 <option value="optionCool" selected="True">cool</option>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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405 <option value="optionH5">h5</option>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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406 <option value="optionHomer">Homer</option>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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407 <option value="optionHicpro">HiCPro</option>
20
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parents: 19
diff changeset
408 <option value="option2Dtext">2D-text</option>
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 19
diff changeset
409
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents: 19
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410
12
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diff changeset
411 </param>
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412 <when value="optionCool">
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413 <expand macro='matrix_h5_cooler_multiple_macro' />
18
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iuc
parents: 17
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414 <param name='correctionName' type='text' label='Correction factors column name' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
415 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 17
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416 <param name='chromosome' type='text' label='Load only one chromosome' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 17
diff changeset
417 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
12
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418 </when>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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419 <when value="optionH5">
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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420 <expand macro='matrix_h5_cooler_multiple_macro' />
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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421 </when>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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422 <when value="optionHomer">
18
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iuc
parents: 17
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423 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
12
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424 </when>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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425 <when value="optionHicpro">
18
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parents: 17
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426 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 17
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427 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
12
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
428 </when>
20
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parents: 19
diff changeset
429 <when value="option2Dtext">
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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430 <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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431
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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432 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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433 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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434 </param>
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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435 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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436 </when>
12
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437 </conditional>
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438 </xml>
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439 <xml name='convertFormat_single_output_macro'>
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440 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
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441 <conditional name="outputFormat_conditional">
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442 <param name="outputFormat_selector" type="select" label="Choose output file type">
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443 <option value="cool" selected="True">cool</option>
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444 <option value="h5">h5</option>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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445 <option value="homer">Homer</option>
6b7987d22eab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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446 <option value="ginteractions">ginteractions</option>
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parents: 19
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447 <option value="hicpro">hicpro</option>
ec4b948dc6f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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parents: 19
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448
12
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449 </param>
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450 <when value="cool">
18
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451 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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452 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
12
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453 </when>
18
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454 <when value='h5' />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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455 <when value='homer' />
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parents: 17
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456 <when value='ginteractions' />
20
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parents: 19
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457 <when value='hicpro' />
12
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458 </conditional>
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diff changeset
459 </xml>
0
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460 <token name="@REFERENCES@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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461
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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462 .. class:: infomark
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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463
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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464 For more information on the tools, please visit our `help site`_.
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465
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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466 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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467
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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468 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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469
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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470 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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471 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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472 .. _help site: https://hicexplorer.readthedocs.org
0
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473
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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474 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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475
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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476 <xml name="multiple_input_bams">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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477 <repeat name="input_files" title="BAM files" min="2">
18
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478 <param name="bamfile" type="data" format="bam" label="BAM file" />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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479 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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480 </repeat>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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481 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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482
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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483 <xml name="multiple_input_bigwigs">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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484 <repeat name="input_files" title="BigWig files" min="2">
18
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diff changeset
485 <param name="bigwigfile" type="data" format="bigwig" label="Bigwig file" />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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486 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead.">
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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487 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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488 </param>
0
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489 </repeat>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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490 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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491
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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492 <xml name="plotTitle">
18
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493 <param name="plotTitle" type="text" value="" optional="True" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. (--plotTitle)">
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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diff changeset
494 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
495 </param>
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
496 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
497
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
498 <token name="@multiple_input_bams@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
499 #import tempfile
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
500 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
501 #set files=[]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
502 #set labels=[]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
503 #for $i in $input_files:
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
504 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
505 #set $temp_input_path = $temp_input_handle.name
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
506 #silent $temp_input_handle.close()
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
507 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
508 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
509 #silent $files.append('%s.bam' % $temp_input_path)
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
510
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
511 ##set $files += [str($i.bamfile)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
512 #if str($i.label.value) != "":
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
513 #set $labels += ["\"%s\"" % ($i.label.value)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
514 #else
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
515 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
516 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
517 #end for
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
518 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
519
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
520 <token name="@multiple_input_bigwigs@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
521 #import tempfile
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
522 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
523 #set files=[]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
524 #set labels=[]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
525 #for $i in $input_files:
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
526 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
aab371aa615e 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 $temp_input_path = $temp_input_handle.name
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
528 #silent $temp_input_handle.close()
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
529 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
530 #silent $files.append('%s.bw' % $temp_input_path)
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
531
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
532 ##set $files += [str($i.bigwigfile)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
533 #if str($i.label.value) != "":
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
534 #set $labels += ["\"%s\"" % ($i.label.value)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
535 #else
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
536 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
537 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
538 #end for
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
539 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
540
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
541 <xml name="reference_genome_source">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
542 <conditional name="source">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
543 <param name="ref_source" type="select" label="Reference genome">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
544 <option value="cached">locally cached</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
545 <option value="history">in your history</option>
aab371aa615e 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>
aab371aa615e 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 value="cached">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
548 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
549 <options from_data_table="deepTools_seqs">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
550 <filter type="sort_by" column="1" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
551 <validator type="no_options" message="No indexes are available." />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
552 </options>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
553 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
554 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
555 <when value="history">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
556 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
557 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
558 </conditional>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
559 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
560
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
561 <token name="@reference_genome_source@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
562 #if $source.ref_source=="history":
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
563 --genome $source.input1
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
564 #else:
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
565 --genome "${source.input1_2bit.fields.path}"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
566 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
567 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
568
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
569 <xml name="effectiveGenomeSize">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
570 <conditional name="effectiveGenomeSize">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
571 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" 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.
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
572 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
573 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.">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
574 <option value="93260000">ce10 (93260000)</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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575 <option value="121400000">dm3 (121400000)</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
576 <option value="2451960000" selected="true">hg19 (2451960000)</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
577 <option value="2150570000">mm9 (2150570000)</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
578 <option value="specific">user specified</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
579 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
580 <when value="specific">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
581 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000" />
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
582 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
583 <when value="2150570000" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
584 <when value="2451960000" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
585 <when value="121400000" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
586 <when value="93260000" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
587 </conditional>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
588 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
589
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
590 <xml name="image_file_format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
591 <param name="outFileFormat" type="select" label="Image file format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
592 <option value="png" selected="true">png</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
593 <option value="pdf">pdf</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
594 <option value="svg">svg</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
595 <option value="eps">eps</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
596 <option value="emf">emf</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
597 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
598 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
599
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
600 <xml name="missingDataAsZero">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
601 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Treat missing data as zero" 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." />
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
602 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
603
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
604 <xml name="input_save_matrix_values">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
605 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" />
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
606 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
607
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
608 <xml name="input_graphic_output_settings">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
609 <conditional name="output">
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
610 <param name="showOutputSettings" type="select" label="Show advanced output settings">
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
611 <option value="no" selected="true">no</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
612 <option value="yes">yes</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
613 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
614 <when value="no" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
615 <when value="yes">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
616 <yield />
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
617 <param name="saveData" type="boolean" label="Save the data underlying the average profile" />
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 17
diff changeset
618 <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." />
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
619 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
620 </conditional>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
621 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
622
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
623 <xml name="input_image_file_format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
624 <param name="outFileFormat" type="select" label="Image file format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
625 <option value="png" selected="true">png</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
626 <option value="pdf">pdf</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
627 <option value="svg">svg</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
628 <option value="eps">eps</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
629 <option value="emf">emf</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
630 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
631 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
632
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
633 <xml name="output_image_file_format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
634 <data format="png" name="outFileName" label="${tool.name} image">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
635 <change_format>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
636 <when input="output.outFileFormat" value="pdf" format="pdf" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
637 <when input="output.outFileFormat" value="svg" format="svg" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
638 <when input="output.outFileFormat" value="eps" format="eps" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
639 <when input="output.outFileFormat" value="emf" format="emf" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
640 </change_format>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
641 </data>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
642 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
643
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
644 <xml name="output_save_matrix_values">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
645 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
646 <filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
647 ((
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
648 output['showOutputSettings'] == 'yes' and
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
649 output['saveMatrix'] is True
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
650 ))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
651 </filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
652 </data>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
653 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
654
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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655 <xml name="output_graphic_outputs">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
656 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
657 <filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
658 ((
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
659 output['showOutputSettings'] == 'yes' and
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
660 output['saveData'] is True
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
661 ))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
662 </filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
663 </data>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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664 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
665 <filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
666 ((
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
667 output['showOutputSettings'] == 'yes' and
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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668 output['saveSortedRegions'] is True
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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669 ))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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670 </filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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671 </data>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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672 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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673
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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674 <xml name="track_input_h5_macro">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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675 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" />
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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676 </xml>
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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677 <xml name="track_input_bed_macro">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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678 <param name="track_input_bed" type="data" format="bed" label="Track file BED format" />
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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679 </xml>
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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680 <xml name="track_input_bedgraph_macro">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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681 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" />
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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682 </xml>
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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683 <xml name="track_input_bigwig_macro">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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684 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" />
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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685 </xml>
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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686 <xml name="track_input_bedgraph_matrix_macro">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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687 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" />
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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688 </xml>
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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689 <xml name="track_input_tabular_macro">
18
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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690 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" />
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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691 </xml>
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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692 <xml name="plot_title">
18
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693 <param name="title" type="text" optional="true" label="Plot title">
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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694 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
d404277cc87a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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695 </param>
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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696 </xml>
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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697
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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698 <xml name="spacer_macro">
18
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699 <param name="spacer_width" type="float" value="" min="0" optional="True" label="Include spacer at the end of the track" help="Width of the spacer." />
2
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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700 </xml>
a9c1d76b90c4 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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701 <xml name="fontsize_macro">
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702 <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" />
2
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703 </xml>
0
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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704 </macros>