Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate macros.xml @ 26:891202c51263 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author iuc
date Thu, 05 Dec 2024 17:54:53 +0000
parents 65558d578f4f
children
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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@">3.7.6</token>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5 <token name="@PROFILE@">23.0</token>
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6 <token name="@USE_RANGE@">
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7 #if $use_range.select_use_range == "yes_use_range":
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8 --range $use_range.range_min:$use_range.range_max
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9 #end if
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10 </token>
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12 <xml name="requirements">
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13 <requirements>
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14 <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement>
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15 <yield />
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16 </requirements>
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17 <version_command>@BINARY@ --version</version_command>
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18 </xml>
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20 <token name="@CHROMOSOME_LIST@">
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21 #if $chromosome_list:
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22 #set $chromosomes = []
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23 #for $chrom in $chromosome_list:
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24 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
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25 #end for
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26 #set $chromosome_string = ' '.join($chromosomes)
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27 --chromosomes $chromosome_string
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28 #end if
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29 </token>
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31 <xml name="chromosome_list">
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32 <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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33 <param argument="--chromosomes" type="text" value="">
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34 <validator type="empty_field" />
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35 </param>
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36 </repeat>
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37 </xml>
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38
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39 <xml name="citations">
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40 <citations>
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41 <citation type="doi">10.1093/nar/gkaa220</citation>
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42 <citation type="doi">10.1093/nar/gky504</citation>
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43 <yield />
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44 </citations>
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45 </xml>
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46 <xml name="dpi">
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47 <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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48 </xml>
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e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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50 <xml name="restrictionCutFile">
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51 <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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52 (i.e. the region between one restriction site and the next)." />
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53 </xml>
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55 <xml name="restrictionSequence">
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56 <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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57 &quot;dangling-ends&quot;. If not given, such statistics will not be available.">
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58 <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator>
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59 </param>
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60 </xml>
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61 <xml name="danglingSequence">
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62 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
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63 Each restriction enzyme recognizes a different DNA sequence and,
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64 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
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65 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
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66 For DpnII, the restriction site and dangling end sequence are the same: GATC.
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67 This information is easily found on the description of the restriction enzyme.
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68 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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69 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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70 <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator>
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71 </param>
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72 </xml>
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74 <xml name="zMax">
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75 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />
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76 <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
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77 </xml>
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78 <xml name="use_range">
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79 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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80 <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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81 <option value="no_use_range">No restriction</option>
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82 <option value="yes_use_range">Only consider counts within a range</option>
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83 </param>
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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84 <when value="no_use_range" />
9
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85 <when value="yes_use_range">
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86 <expand macro='range' />
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87 </when>
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88 </conditional>
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89 </xml>
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90
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91 <xml name="range">
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e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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92 <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." />
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93 <param name='range_max' type="integer" value="" min="0" label="Maximum range to consider interactions" />
9
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94 </xml>
0
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95
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96 <xml name="colormap">
5
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97 <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">
1
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98 <option value="RdYlBu">RdYlBu</option>
0
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99 <option value="Accent">Accent</option>
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100 <option value="Spectral">Spectral</option>
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101 <option value="Set1">Set1</option>
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102 <option value="Set2">Set2</option>
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103 <option value="Set3">Set3</option>
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104 <option value="Dark2">Dark2</option>
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105 <option value="Reds">Reds</option>
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106 <option value="Oranges">Oranges</option>
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107 <option value="Greens">Greens</option>
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108 <option value="Blues">Blues</option>
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109 <option value="Greys">Greys</option>
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110 <option value="Purples">Purples</option>
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111 <option value="Paired">Paired</option>
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112 <option value="Pastel1">Pastel1</option>
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113 <option value="Pastel2">Pastel2</option>
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114 <option value="spring">spring</option>
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115 <option value="summer">summer</option>
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116 <option value="autumn">autumn</option>
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117 <option value="winter">winter</option>
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118 <option value="hot">hot</option>
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119 <option value="coolwarm">coolwarm</option>
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120 <option value="cool">cool</option>
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121 <option value="seismic">seismic</option>
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122 <option value="terrain">terrain</option>
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123 <option value="ocean">ocean</option>
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124 <option value="rainbow">rainbow</option>
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125 <option value="bone">bone</option>
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126 <option value="flag">flag</option>
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127 <option value="prism">prism</option>
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128 <option value="cubehelix">cubehelix</option>
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129 <option value="binary">binary</option>
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130 <option value="pink">pink</option>
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131 <option value="gray">gray</option>
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132 <option value="copper">copper</option>
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133 <option value="BrBG">BrBG</option>
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134 <option value="BuGn">BuGn</option>
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135 <option value="BuPu">BuPu</option>
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136 <option value="GnBu">GnBu</option>
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137 <option value="OrRd">OrRd</option>
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138 <option value="PiYG">PiYG</option>
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139 <option value="PRGn">PRGn</option>
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140 <option value="PuOr">PuOr</option>
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141 <option value="PuRd">PuRd</option>
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142 <option value="PuBu">PuBu</option>
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143 <option value="RdBu">RdBu</option>
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144 <option value="RdGy">RdGy</option>
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145 <option value="RdPu">RdPu</option>
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146 <option value="YlGn">YlGn</option>
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147 <option value="PuBuGn">PuBuGn</option>
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148 <option value="RdYlGn">RdYlGn</option>
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149 <option value="YlGnBu">YlGnBu</option>
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150 <option value="YlOrBr">YlOrBr</option>
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151 <option value="YlOrRd">YlOrRd</option>
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152 <option value="gist_gray">gist_gray</option>
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153 <option value="gist_stern">gist_stern</option>
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154 <option value="gist_earth">gist_earth</option>
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155 <option value="gist_yarg">gist_yarg</option>
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156 <option value="gist_ncar">gist_ncar</option>
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157 <option value="gist_rainbow">gist_rainbow</option>
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158 <option value="gist_heat">gist_heat</option>
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159 <option value="gnuplot">gnuplot</option>
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160 <option value="gnuplot2">gnuplot2</option>
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161 <option value="CMRmap">CMRmap</option>
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162 <option value="bwr">bwr</option>
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163 <option value="hsv">hsv</option>
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164 <option value="brg">brg</option>
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165 <option value="jet">jet</option>
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166 <option value="afmhot">afmhot</option>
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
167 <option value="plasma">plasma</option>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
168 <option value="Accent_r">Accent reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
169 <option value="Spectral_r">Spectral reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
170 <option value="Set1_r">Set1 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
171 <option value="Set2_r">Set2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
172 <option value="Set3_r">Set3 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
173 <option value="Dark2_r">Dark2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
174 <option value="Reds_r">Reds reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
175 <option value="Oranges_r">Oranges reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
176 <option value="Greens_r">Greens reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
177 <option value="Blues_r">Blues reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
178 <option value="Greys_r">Greys reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
179 <option value="Purples_r">Purples reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
180 <option value="Paired_r">Paired reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
181 <option value="Pastel1_r">Pastel1 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
182 <option value="Pastel2_r">Pastel2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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183 <option value="spring_r">spring reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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184 <option value="summer_r">summer reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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185 <option value="autumn_r">autumn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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186 <option value="winter_r">winter reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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187 <option value="hot_r">hot reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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188 <option value="coolwarm_r">coolwarm reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
189 <option value="cool_r">cool reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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190 <option value="seismic_r">seismic reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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191 <option value="terrain_r">terrain reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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192 <option value="ocean_r">ocean reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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193 <option value="rainbow_r">rainbow reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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194 <option value="bone_r">bone reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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195 <option value="flag_r">flag reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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196 <option value="prism_r">prism reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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197 <option value="cubehelix_r">cubehelix reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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198 <option value="binary_r">binary reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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199 <option value="pink_r">pink reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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200 <option value="gray_r">gray reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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201 <option value="copper_r">copper reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
202 <option value="BrBG_r">BrBG reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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203 <option value="BuGn_r">BuGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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204 <option value="BuPu_r">BuPu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
205 <option value="GnBu_r">GnBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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206 <option value="OrRd_r">OrRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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207 <option value="PiYG_r">PiYG reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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208 <option value="PRGn_r">PRGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
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209 <option value="PuOr_r">PuOr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
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210 <option value="PuRd_r">PuRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
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211 <option value="PuBu_r">PuBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
212 <option value="RdBu_r">RdBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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213 <option value="RdGy_r">RdGy reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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214 <option value="RdPu_r">RdPu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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215 <option value="YlGn_r">YlGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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216 <option value="PuBuGn_r">PuBuGn reversed</option>
1
a6ccec9faaa3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
217 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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218 <option value="RdYlGn_r">RdYlGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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219 <option value="YlGnBu_r">YlGnBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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220 <option value="YlOrBr_r">YlOrBr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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221 <option value="YlOrRd_r">YlOrRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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222 <option value="gist_gray_r">gist_gray reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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223 <option value="gist_stern_r">gist_stern reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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224 <option value="gist_earth_r">gist_earth reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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225 <option value="gist_yarg_r">gist_yarg reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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226 <option value="gist_ncar_r">gist_ncar reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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227 <option value="gist_rainbow_r">gist_rainbow reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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228 <option value="gist_heat_r">gist_heat reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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229 <option value="gnuplot_r">gnuplot reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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230 <option value="gnuplot2_r">gnuplot2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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231 <option value="CMRmap_r">CMRmap reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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232 <option value="bwr_r">bwr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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233 <option value="hsv_r">hsv reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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234 <option value="brg_r">brg reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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235 <option value="jet_r">jet reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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236 <option value="afmhot_r">afmhot reversed</option>
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
237 <option value="plasma_r">plasma reversed</option>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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238 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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239 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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240
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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241 <xml name="multiple_input_matrices">
10
551510b684b7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 9
diff changeset
242 <repeat name="input_files" title="Hi-C Matrix files" min="2">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
243 <param name="matrix" type="data" format="h5,cool" label="Hi-C Matrix file" help="" />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
244 <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
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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245 </repeat>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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246 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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247
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248 <token name="@multiple_input_matrices@">
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249 #set $matrices = []
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250 #set $mlabels = []
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251 #for $counter, $i in enumerate($input_files):
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252 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
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253 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
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254
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255 #if str($i.mlabel.value) != "":
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256 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
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257 #else
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258 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
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259 #end if
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260 #end for
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261 #set $mlabels = ' '.join($mlabels)
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262 #set $matrices = ' '.join($matrices)
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263 </token>
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264
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265 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
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266 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
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267 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
0
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268
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269 <xml name="region">
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270 <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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271 <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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272 </param>
0
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273 </xml>
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274
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275 <xml name="kmeans_clustering">
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276 <conditional name="used_multiple_regions">
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277 <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.">
0
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278 <option value="yes">Yes, I used multiple groups of regions</option>
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279 <option value="no">No, I used only one group</option>
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280 </param>
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281 <when value="no">
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282 <conditional name="clustering">
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283 <param name="clustering_options" type="select" label="Clustering algorithm">
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284 <option value="none">No clustering</option>
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285 <option value="kmeans">Kmeans clustering</option>
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286 </param>
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287 <when value="kmeans">
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288 <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)." />
0
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289 </when>
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290 <when value="none" />
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291 </conditional>
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292 </when>
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293 <when value="yes" />
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294 </conditional>
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295 </xml>
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296
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297 <token name="@KMEANS_CLUSTERING@">
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298 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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299 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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300 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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301 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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302 #end if
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303 #end if
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304 #end if
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305 </token>
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306
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307 <xml name="samFlag">
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308 <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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309 </xml>
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310 <xml name="plotNumbers">
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311 <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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312 </xml>
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313 <xml name="doNotExtendPairedEnds">
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314 <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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315 </xml>
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316 <xml name="ignoreDuplicates">
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317 <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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318 </xml>
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319 <xml name="minMappingQuality">
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320 <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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321 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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322 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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323 </xml>
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324
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325 <xml name="skipZeros">
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326 <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)" />
0
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327 </xml>
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328
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329 <xml name="fragmentLength">
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330 <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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331 </xml>
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332
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333 <xml name="scaleFactor">
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334 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)" />
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335 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
0
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336 </xml>
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337 <xml name="xMax">
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338 <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
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339 </xml>
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340 <xml name="filterThreshold">
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341 <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." />
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342 <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." />
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343 </xml>
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344 <xml name="pseudocount">
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345 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero." />
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346 </xml>
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347 <xml name='matrix_h5_cooler_macro'>
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348 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" />
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349 </xml>
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350 <xml name='matrix_h5_cooler_multiple_macro'>
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351 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
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352 </xml>
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353
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354 <xml name='matrix_cooler_multiple_macro'>
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355 <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
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356 </xml>
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357 <xml name='convertFormat_single_macro'>
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358 <conditional name="inputFormat_conditional">
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359 <param name="inputFormat_selector" type="select" label="Choose input file type">
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360 <option value="optionCool" selected="True">cool</option>
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361 <option value="optionH5">h5</option>
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362 <option value="optionHic">hic</option>
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363 <option value="optionHomer">Homer</option>
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364 <option value="optionHicpro">HiCPro</option>
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365 <option value="option2Dtext">2D-text</option>
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366
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367 </param>
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368 <when value="optionCool">
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369 <expand macro='matrix_h5_cooler_macro' />
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370 <param name='correctionName' type='text' label='Correction factors column name' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
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372 <param name='chromosome' type='text' label='Load only one chromosome' />
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373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
16
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374 </when>
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375 <when value="optionH5">
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376 <expand macro='matrix_h5_cooler_macro' />
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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377 </when>
17
e1204b7a4516 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 0f4a6baff82058bb67678f402d302e2b8964f750"
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378 <when value="optionHic">
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379 <param name='matrixHic' type='data' format='hic' label='.hic matrix' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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380 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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381 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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382 </param>
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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383 </when>
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384 <when value="optionHomer">
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385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
16
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386 </when>
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387 <when value="optionHicpro">
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388 <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
22
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389 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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390 </when>
24
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391 <when value="option2Dtext">
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392 <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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393
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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394 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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395 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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396 </param>
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397 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
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398 </when>
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399 </conditional>
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400 </xml>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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401
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
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402 <xml name='convertFormat_multiple_macro'>
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403 <conditional name="inputFormat_conditional">
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404 <param name="inputFormat_selector" type="select" label="Choose input file type">
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405 <option value="optionCool" selected="True">cool</option>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
406 <option value="optionH5">h5</option>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
407 <option value="optionHomer">Homer</option>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
408 <option value="optionHicpro">HiCPro</option>
24
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iuc
parents: 23
diff changeset
409 <option value="option2Dtext">2D-text</option>
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
diff changeset
410
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
diff changeset
411
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
412 </param>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
413 <when value="optionCool">
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
414 <expand macro='matrix_h5_cooler_multiple_macro' />
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
415 <param name='correctionName' type='text' label='Correction factors column name' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
416 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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417 <param name='chromosome' type='text' label='Load only one chromosome' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
418 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
419 </when>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
420 <when value="optionH5">
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
421 <expand macro='matrix_h5_cooler_multiple_macro' />
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
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422 </when>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
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423 <when value="optionHomer">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
424 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
425 </when>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
426 <when value="optionHicpro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
427 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
428 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
429 </when>
24
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
diff changeset
430 <when value="option2Dtext">
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
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431 <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
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432
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
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433 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
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434 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
diff changeset
435 </param>
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
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436 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
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437 </when>
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
438 </conditional>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
439 </xml>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
440 <xml name='convertFormat_single_output_macro'>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
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441 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
442 <conditional name="outputFormat_conditional">
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
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443 <param name="outputFormat_selector" type="select" label="Choose output file type">
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
444 <option value="cool" selected="True">cool</option>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
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445 <option value="h5">h5</option>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
446 <option value="homer">Homer</option>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
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447 <option value="ginteractions">ginteractions</option>
24
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
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448 <option value="hicpro">hicpro</option>
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 23
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449
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
450 </param>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
451 <when value="cool">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
452 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
453 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
454 </when>
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
455 <when value='h5' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
456 <when value='homer' />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
457 <when value='ginteractions' />
24
0147ee498251 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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parents: 23
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458 <when value='hicpro' />
16
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
459 </conditional>
3a7698050cb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 15
diff changeset
460 </xml>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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461 <token name="@REFERENCES@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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462
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
463 .. class:: infomark
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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464
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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465 For more information on the tools, please visit our `help site`_.
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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466
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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467 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
468
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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469 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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470
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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471 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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472 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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473 .. _help site: https://hicexplorer.readthedocs.org
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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474
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
475 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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476
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
477 <xml name="multiple_input_bams">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
478 <repeat name="input_files" title="BAM files" min="2">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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479 <param name="bamfile" type="data" format="bam" label="BAM file" />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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480 <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
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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481 </repeat>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
482 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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483
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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484 <xml name="multiple_input_bigwigs">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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485 <repeat name="input_files" title="BigWig files" min="2">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
486 <param name="bigwigfile" type="data" format="bigwig" label="Bigwig file" />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 21
diff changeset
487 <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.">
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
488 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
489 </param>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
490 </repeat>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
491 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
492
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
493 <xml name="plotTitle">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
494 <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)">
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
495 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
496 </param>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
497 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
498
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
499 <token name="@multiple_input_bams@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
500 #import tempfile
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
501 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
502 #set files=[]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
503 #set labels=[]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
504 #for $i in $input_files:
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
505 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
506 #set $temp_input_path = $temp_input_handle.name
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
507 #silent $temp_input_handle.close()
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
508 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
509 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
510 #silent $files.append('%s.bam' % $temp_input_path)
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
511
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
512 ##set $files += [str($i.bamfile)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
513 #if str($i.label.value) != "":
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
514 #set $labels += ["\"%s\"" % ($i.label.value)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
515 #else
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
516 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
517 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
518 #end for
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
519 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
520
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
521 <token name="@multiple_input_bigwigs@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
522 #import tempfile
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
523 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
524 #set files=[]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
525 #set labels=[]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
526 #for $i in $input_files:
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
527 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
528 #set $temp_input_path = $temp_input_handle.name
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
529 #silent $temp_input_handle.close()
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
530 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
531 #silent $files.append('%s.bw' % $temp_input_path)
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
532
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
533 ##set $files += [str($i.bigwigfile)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
534 #if str($i.label.value) != "":
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
535 #set $labels += ["\"%s\"" % ($i.label.value)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
536 #else
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
537 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
538 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
539 #end for
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
540 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
541
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
542 <xml name="reference_genome_source">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
543 <conditional name="source">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
544 <param name="ref_source" type="select" label="Reference genome">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
545 <option value="cached">locally cached</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
546 <option value="history">in your history</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
547 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
548 <when value="cached">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
549 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
550 <options from_data_table="deepTools_seqs">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
551 <filter type="sort_by" column="1" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
552 <validator type="no_options" message="No indexes are available." />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
553 </options>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
554 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
555 </when>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
556 <when value="history">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
557 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
558 </when>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
559 </conditional>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
560 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
561
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
562 <token name="@reference_genome_source@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
563 #if $source.ref_source=="history":
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
564 --genome $source.input1
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
565 #else:
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
566 --genome "${source.input1_2bit.fields.path}"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
567 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
568 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
569
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
570 <xml name="effectiveGenomeSize">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
571 <conditional name="effectiveGenomeSize">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
diff changeset
572 <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
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573 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
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574 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.">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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575 <option value="93260000">ce10 (93260000)</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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576 <option value="121400000">dm3 (121400000)</option>
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577 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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578 <option value="2150570000">mm9 (2150570000)</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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579 <option value="specific">user specified</option>
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580 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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581 <when value="specific">
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e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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582 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000" />
0
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583 </when>
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584 <when value="2150570000" />
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585 <when value="2451960000" />
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586 <when value="121400000" />
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587 <when value="93260000" />
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588 </conditional>
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589 </xml>
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590
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591 <xml name="image_file_format">
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592 <param name="outFileFormat" type="select" label="Image file format">
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593 <option value="png" selected="true">png</option>
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594 <option value="pdf">pdf</option>
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595 <option value="svg">svg</option>
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596 <option value="eps">eps</option>
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597 <option value="emf">emf</option>
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598 </param>
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599 </xml>
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600
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601 <xml name="missingDataAsZero">
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602 <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
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603 </xml>
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604
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605 <xml name="input_save_matrix_values">
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parents: 21
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606 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" />
0
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607 </xml>
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diff changeset
608
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609 <xml name="input_graphic_output_settings">
22
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parents: 21
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610 <conditional name="output">
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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parents: 21
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611 <param name="showOutputSettings" type="select" label="Show advanced output settings">
0
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612 <option value="no" selected="true">no</option>
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613 <option value="yes">yes</option>
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614 </param>
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615 <when value="no" />
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616 <when value="yes">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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617 <yield />
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parents: 21
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618 <param name="saveData" type="boolean" label="Save the data underlying the average profile" />
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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619 <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
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620 </when>
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621 </conditional>
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622 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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623
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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624 <xml name="input_image_file_format">
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625 <param name="outFileFormat" type="select" label="Image file format">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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626 <option value="png" selected="true">png</option>
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627 <option value="pdf">pdf</option>
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628 <option value="svg">svg</option>
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629 <option value="eps">eps</option>
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630 <option value="emf">emf</option>
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631 </param>
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632 </xml>
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633
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634 <xml name="output_image_file_format">
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635 <data format="png" name="outFileName" label="${tool.name} image">
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636 <change_format>
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637 <when input="output.outFileFormat" value="pdf" format="pdf" />
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638 <when input="output.outFileFormat" value="svg" format="svg" />
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639 <when input="output.outFileFormat" value="eps" format="eps" />
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640 <when input="output.outFileFormat" value="emf" format="emf" />
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641 </change_format>
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642 </data>
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643 </xml>
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644
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645 <xml name="output_save_matrix_values">
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646 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
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647 <filter>
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648 ((
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649 output['showOutputSettings'] == 'yes' and
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650 output['saveMatrix'] is True
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651 ))
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652 </filter>
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653 </data>
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654 </xml>
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655
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656 <xml name="output_graphic_outputs">
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657 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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658 <filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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659 ((
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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660 output['showOutputSettings'] == 'yes' and
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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diff changeset
661 output['saveData'] is True
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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662 ))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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663 </filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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664 </data>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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665 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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666 <filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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667 ((
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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668 output['showOutputSettings'] == 'yes' and
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
669 output['saveSortedRegions'] is True
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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670 ))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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671 </filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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672 </data>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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673 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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674
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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675 <xml name="track_input_h5_macro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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676 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" />
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
677 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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678 <xml name="track_input_bed_macro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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679 <param name="track_input_bed" type="data" format="bed" label="Track file BED format" />
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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680 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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681 <xml name="track_input_bedgraph_macro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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682 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" />
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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683 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
684 <xml name="track_input_bigwig_macro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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685 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" />
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
686 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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687 <xml name="track_input_bedgraph_matrix_macro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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688 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" />
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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689 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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690 <xml name="track_input_tabular_macro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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691 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" />
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
692 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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693 <xml name="plot_title">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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694 <param name="title" type="text" optional="true" label="Plot title">
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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695 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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696 </param>
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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697 </xml>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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698
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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699 <xml name="spacer_macro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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700 <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." />
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
701 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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702 <xml name="fontsize_macro">
22
e7e5855492df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 21
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703 <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" />
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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704 </xml>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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705 </macros>