hicexplorer_hicaggregatecontacts: macros.xml annotate

annotate macros.xml @ 1:ec59bf4c3d06 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8

author	iuc
date	Fri, 27 Apr 2018 03:32:37 -0400
parents	ccd1d3013827
children	a48457358aa8

rev	line source
0 ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	1 <macros>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
1 ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 0 diff changeset	3 <token name="@WRAPPER_VERSION@">2.1.2</token>
0 ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	4 <token name="@USE_RANGE@">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	5 #if $use_range.select_use_range == "yes_use_range":
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	6 --range $range_min:$range_max
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	7 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	8 </token>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	9
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	10 <xml name="requirements">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	11 <requirements>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	13 <yield />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	14 </requirements>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	15 <version_command>@BINARY@ --version</version_command>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	16 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	17
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	18 <xml name="citations">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	19 <citations>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	20 <citation type="doi">10.5281/zenodo.1133705</citation>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	21 <yield />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	22 </citations>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	23 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	24
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	25 <xml name="zMax">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	26 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	27 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	28 <xml name="use_range">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	29 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
1 ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 0 diff changeset	30 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
0 ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	31 <option value="no_use_range">No restriction</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	32 <option value="yes_use_range">Only consider counts within a range</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	33 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	34 <when value="no_use_range"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	35 <when value="yes_use_range">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	36 <expand macro='range' />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	37 </when>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	38 </conditional>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	39 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	40
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	41 <xml name="range">
1 ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 0 diff changeset	42 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 0 diff changeset	43 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
0 ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	44 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	45
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	46 <xml name="colormap">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	47 <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">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	48 <option value="RdYlBu">RdYlBu</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	49 <option value="Accent">Accent</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	50 <option value="Spectral">Spectral</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	51 <option value="Set1">Set1</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	52 <option value="Set2">Set2</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	53 <option value="Set3">Set3</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	54 <option value="Dark2">Dark2</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	55 <option value="Reds">Reds</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	56 <option value="Oranges">Oranges</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	57 <option value="Greens">Greens</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	58 <option value="Blues">Blues</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	59 <option value="Greys">Greys</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	60 <option value="Purples">Purples</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	61 <option value="Paired">Paired</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	62 <option value="Pastel1">Pastel1</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	63 <option value="Pastel2">Pastel2</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	64 <option value="spring">spring</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	65 <option value="summer">summer</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	66 <option value="autumn">autumn</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	67 <option value="winter">winter</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	68 <option value="hot">hot</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	69 <option value="coolwarm">coolwarm</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	70 <option value="cool">cool</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	71 <option value="seismic">seismic</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	72 <option value="terrain">terrain</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	73 <option value="ocean">ocean</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	74 <option value="rainbow">rainbow</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	75 <option value="bone">bone</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	76 <option value="flag">flag</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	77 <option value="prism">prism</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	78 <option value="cubehelix">cubehelix</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	79 <option value="binary">binary</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	80 <option value="pink">pink</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	81 <option value="gray">gray</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	82 <option value="copper">copper</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	83 <option value="BrBG">BrBG</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	84 <option value="BuGn">BuGn</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	85 <option value="BuPu">BuPu</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	86 <option value="GnBu">GnBu</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	87 <option value="OrRd">OrRd</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	88 <option value="PiYG">PiYG</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	89 <option value="PRGn">PRGn</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	90 <option value="PuOr">PuOr</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	91 <option value="PuRd">PuRd</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	92 <option value="PuBu">PuBu</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	93 <option value="RdBu">RdBu</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	94 <option value="RdGy">RdGy</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	95 <option value="RdPu">RdPu</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	96 <option value="YlGn">YlGn</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	97 <option value="PuBuGn">PuBuGn</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	98 <option value="RdYlGn">RdYlGn</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	99 <option value="YlGnBu">YlGnBu</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	100 <option value="YlOrBr">YlOrBr</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	101 <option value="YlOrRd">YlOrRd</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	102 <option value="gist_gray">gist_gray</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	103 <option value="gist_stern">gist_stern</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	104 <option value="gist_earth">gist_earth</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	105 <option value="gist_yarg">gist_yarg</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	106 <option value="gist_ncar">gist_ncar</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	107 <option value="gist_rainbow">gist_rainbow</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	108 <option value="gist_heat">gist_heat</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	109 <option value="gnuplot">gnuplot</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	110 <option value="gnuplot2">gnuplot2</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	111 <option value="CMRmap">CMRmap</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	112 <option value="bwr">bwr</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	113 <option value="hsv">hsv</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	114 <option value="brg">brg</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	115 <option value="jet">jet</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	116 <option value="afmhot">afmhot</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	117 <option value="Accent_r">Accent reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	118 <option value="Spectral_r">Spectral reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	119 <option value="Set1_r">Set1 reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	120 <option value="Set2_r">Set2 reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	121 <option value="Set3_r">Set3 reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	122 <option value="Dark2_r">Dark2 reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	123 <option value="Reds_r">Reds reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	124 <option value="Oranges_r">Oranges reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	125 <option value="Greens_r">Greens reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	126 <option value="Blues_r">Blues reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	127 <option value="Greys_r">Greys reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	128 <option value="Purples_r">Purples reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	129 <option value="Paired_r">Paired reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	130 <option value="Pastel1_r">Pastel1 reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	131 <option value="Pastel2_r">Pastel2 reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	132 <option value="spring_r">spring reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	133 <option value="summer_r">summer reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	134 <option value="autumn_r">autumn reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	135 <option value="winter_r">winter reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	136 <option value="hot_r">hot reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	137 <option value="coolwarm_r">coolwarm reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	138 <option value="cool_r">cool reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	139 <option value="seismic_r">seismic reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	140 <option value="terrain_r">terrain reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	141 <option value="ocean_r">ocean reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	142 <option value="rainbow_r">rainbow reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	143 <option value="bone_r">bone reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	144 <option value="flag_r">flag reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	145 <option value="prism_r">prism reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	146 <option value="cubehelix_r">cubehelix reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	147 <option value="binary_r">binary reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	148 <option value="pink_r">pink reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	149 <option value="gray_r">gray reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	150 <option value="copper_r">copper reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	151 <option value="BrBG_r">BrBG reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	152 <option value="BuGn_r">BuGn reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	153 <option value="BuPu_r">BuPu reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	154 <option value="GnBu_r">GnBu reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	155 <option value="OrRd_r">OrRd reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	156 <option value="PiYG_r">PiYG reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	157 <option value="PRGn_r">PRGn reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	158 <option value="PuOr_r">PuOr reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	159 <option value="PuRd_r">PuRd reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	160 <option value="PuBu_r">PuBu reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	161 <option value="RdBu_r">RdBu reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	162 <option value="RdGy_r">RdGy reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	163 <option value="RdPu_r">RdPu reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	164 <option value="YlGn_r">YlGn reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	165 <option value="PuBuGn_r">PuBuGn reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	167 <option value="RdYlGn_r">RdYlGn reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	168 <option value="YlGnBu_r">YlGnBu reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	169 <option value="YlOrBr_r">YlOrBr reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	170 <option value="YlOrRd_r">YlOrRd reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	171 <option value="gist_gray_r">gist_gray reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	172 <option value="gist_stern_r">gist_stern reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	173 <option value="gist_earth_r">gist_earth reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	174 <option value="gist_yarg_r">gist_yarg reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	175 <option value="gist_ncar_r">gist_ncar reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	176 <option value="gist_rainbow_r">gist_rainbow reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	177 <option value="gist_heat_r">gist_heat reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	178 <option value="gnuplot_r">gnuplot reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	179 <option value="gnuplot2_r">gnuplot2 reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	180 <option value="CMRmap_r">CMRmap reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	181 <option value="bwr_r">bwr reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	182 <option value="hsv_r">hsv reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	183 <option value="brg_r">brg reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	184 <option value="jet_r">jet reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	185 <option value="afmhot_r">afmhot reversed</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	186 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	187 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	188
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	189
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	190 <xml name="multiple_input_matrices">
1 ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 0 diff changeset	191 <repeat name="input_files" title="Hi-C Matrix files" min="2">
0 ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	192 <param name="matrix" type="data" format="h5,cool"
1 ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 0 diff changeset	193 label="Hi-C Matrix file"
0 ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	194 help=""/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	195 <param name="mlabel" type="text" size="30" optional="true" value=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	196 label="Label"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	197 help="Label to use in the output. If not given the dataset name will be used instead."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	198 </repeat>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	199 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	200
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	201 <token name="@multiple_input_matrices@">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	202 #set $matrices = []
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	203 #set $mlabels = []
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	204 #for $counter, $i in enumerate($input_files):
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	205 ln -s $i.matrix #echo str($counter)+'_matrix'#;
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	206 #silent $matrices.append( '%s_matrix' % $counter )
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	207
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	208 #if str($i.mlabel.value) != "":
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	210 #else
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	211 #set $mlabels += ['"%s"' % ($i.matrix.name)]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	212 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	213 #end for
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	214 #set $mlabels = ' '.join($mlabels)
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	215 #set $matrices = ' '.join($matrices)
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	216 </token>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	217
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	218
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	219 <xml name="region">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	220 <param name="region" type="text" label="Region of the genome to limit the operation"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	222 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	223
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	224
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	225
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	226 <xml name="kmeans_clustering">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	227 <conditional name="used_multiple_regions">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	228 <param name="used_multiple_regions_options" type="select"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	229 label="Did you compute the matrix with more than one groups of regions?"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	230 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.">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	231 <option value="yes">Yes, I used multiple groups of regions</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	232 <option value="no">No, I used only one group</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	233 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	234 <when value="no">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	235 <conditional name="clustering">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	236 <param name="clustering_options" type="select" label="Clustering algorithm">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	237 <option value="none">No clustering</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	238 <option value="kmeans">Kmeans clustering</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	239 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	240 <when value="kmeans">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	242 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)."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	243 </when>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	244 <when value="none" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	245 </conditional>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	246 </when>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	247 <when value="yes" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	248 </conditional>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	249 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	250
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	251 <token name="@KMEANS_CLUSTERING@">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	256 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	257 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	258 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	259 </token>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	260
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	261 <xml name="samFlag">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	262 <param name="samFlag" type="integer" optional="true" value=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	263 label="Filter reads based on the SAM flag"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	264 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)"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	265 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	266 <xml name="plotNumbers">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	268 label="Plot the correlation value"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	270 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	271 <xml name="doNotExtendPairedEnds">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	273 label="Do not extend paired ends"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	274 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)"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	275 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	276
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	277 <xml name="ignoreDuplicates">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	279 label="Ignore duplicates"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	280 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)" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	281 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	282
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	283 <xml name="minMappingQuality">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	285 label="Minimum mapping quality"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	286 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	287 Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	288 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."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	289 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	290
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	291 <xml name="skipZeros">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	293 label ="Skip zeros"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	294 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)" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	295 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	296
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	297 <xml name="fragmentLength">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	298 <param name="fragmentLength" type="integer" value="300" min="1"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	299 label="Fragment length used for the sequencing"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	301 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	302
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	303 <xml name="scaleFactor">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	306 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	307
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	308 <xml name="xMax">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	309 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	310 label="Max value for the x-axis in counts per bin" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	311 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	312
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	313 <xml name="filterThreshold">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	315 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	316
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	319 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	320
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	321
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	322 <xml name="pseudocount">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	323 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	324 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	325 <xml name='matrix_h5_cooler_macro'>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	326 <param name='matrix_h5_cooler' type="data" format="h5,cool"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	327 label="Matrix to compute on"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	328 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	329 <xml name='matrix_h5_cooler_multiple_macro'>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	330 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	331 label="Matricies to compute on" multiple="true"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	332 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	333 <token name="@REFERENCES@">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	334
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	335 .. class:: infomark
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	336
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	337 For more information on the tools, please visit our `help site`_.
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	338
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	339 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	340
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	341 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	342
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	343 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	344 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	345 .. _help site: https://hicexplorer.readthedocs.org
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	346
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	347 </token>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	348
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	349
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	350 <xml name="multiple_input_bams">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	351 <repeat name="input_files" title="BAM files" min="2">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	352 <param name="bamfile" type="data" format="bam"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	353 label="Bam file"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	354 help="The BAM file must be sorted."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	355 <param name="label" type="text" size="30" optional="true" value=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	356 label="Label"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	357 help="Label to use in the output. If not given the dataset name will be used instead."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	358 </repeat>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	359 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	360
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	361 <xml name="multiple_input_bigwigs">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	362 <repeat name="input_files" title="BigWig files" min="2">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	363 <param name="bigwigfile" type="data" format="bigwig"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	364 label="Bigwig file"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	365 help="The Bigwig file must be sorted."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	366 <param name="label" type="text" size="30" optional="true" value=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	367 label="Label"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	368 help="Label to use in the output. If not given the dataset name will be used instead."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	369 </repeat>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	370 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	371
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	372 <xml name="plotTitle">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	373 <param name="plotTitle" type="text" value="" size="30" optional="True"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	374 label="Title of the plot"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	375 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	376 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	377
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	378 <token name="@multiple_input_bams@">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	379 #import tempfile
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	380 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	381 #set files=[]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	382 #set labels=[]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	383 #for $i in $input_files:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	385 #set $temp_input_path = $temp_input_handle.name
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	386 #silent $temp_input_handle.close()
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	387 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	388 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	389 #silent $files.append('%s.bam' % $temp_input_path)
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	390
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	391 ##set $files += [str($i.bamfile)]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	392 #if str($i.label.value) != "":
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	393 #set $labels += ["\"%s\"" % ($i.label.value)]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	394 #else
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	395 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	396 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	397 #end for
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	398 </token>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	399
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	400 <token name="@multiple_input_bigwigs@">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	401 #import tempfile
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	402 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	403 #set files=[]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	404 #set labels=[]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	405 #for $i in $input_files:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	406 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	407 #set $temp_input_path = $temp_input_handle.name
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	408 #silent $temp_input_handle.close()
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	409 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	410 #silent $files.append('%s.bw' % $temp_input_path)
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	411
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	412 ##set $files += [str($i.bigwigfile)]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	413 #if str($i.label.value) != "":
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	414 #set $labels += ["\"%s\"" % ($i.label.value)]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	415 #else
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	416 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	417 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	418 #end for
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	419 </token>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	420
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	421 <xml name="reference_genome_source">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	422 <conditional name="source">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	423 <param name="ref_source" type="select" label="Reference genome">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	424 <option value="cached">locally cached</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	425 <option value="history">in your history</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	426 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	427 <when value="cached">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	428 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	429 <options from_data_table="deepTools_seqs">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	430 <filter type="sort_by" column="1" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	431 <validator type="no_options" message="No indexes are available." />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	432 </options>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	433 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	434 </when>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	435 <when value="history">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	436 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	437 </when>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	438 </conditional>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	439 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	440
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	441 <token name="@reference_genome_source@">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	442 #if $source.ref_source=="history":
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	443 --genome $source.input1
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	444 #else:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	445 --genome "${source.input1_2bit.fields.path}"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	446 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	447 </token>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	448
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	449 <xml name="effectiveGenomeSize">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	450 <conditional name="effectiveGenomeSize">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	451 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	452 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.
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	453 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	454 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.">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	455 <option value="93260000">ce10 (93260000)</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	456 <option value="121400000">dm3 (121400000)</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	457 <option value="2451960000" selected="true">hg19 (2451960000)</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	458 <option value="2150570000">mm9 (2150570000)</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	459 <option value="specific">user specified</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	460 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	461 <when value="specific">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	462 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	463 </when>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	464 <when value="2150570000" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	465 <when value="2451960000" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	466 <when value="121400000" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	467 <when value="93260000" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	468 </conditional>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	469 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	470
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	471 <xml name="image_file_format">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	472 <param name="outFileFormat" type="select" label="Image file format">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	473 <option value="png" selected="true">png</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	474 <option value="pdf">pdf</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	475 <option value="svg">svg</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	476 <option value="eps">eps</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	477 <option value="emf">emf</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	478 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	479 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	480
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	481 <xml name="missingDataAsZero">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	482 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	483 label ="Treat missing data as zero"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	484 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." />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	485 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	486
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	487 <xml name="input_save_matrix_values">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	488 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	489 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	490
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	491 <xml name="input_graphic_output_settings">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	492 <conditional name="output" >
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	493 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	494 <option value="no" selected="true">no</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	495 <option value="yes">yes</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	496 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	497 <when value="no" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	498 <when value="yes">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	499 <yield />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	500 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	501 <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."/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	502 </when>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	503 </conditional>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	504 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	505
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	506 <xml name="input_image_file_format">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	507 <param name="outFileFormat" type="select" label="Image file format">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	508 <option value="png" selected="true">png</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	509 <option value="pdf">pdf</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	510 <option value="svg">svg</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	511 <option value="eps">eps</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	512 <option value="emf">emf</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	513 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	514 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	515
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	516 <xml name="output_image_file_format">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	517 <data format="png" name="outFileName" label="${tool.name} image">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	518 <change_format>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	519 <when input="output.outFileFormat" value="pdf" format="pdf" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	520 <when input="output.outFileFormat" value="svg" format="svg" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	521 <when input="output.outFileFormat" value="eps" format="eps" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	522 <when input="output.outFileFormat" value="emf" format="emf" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	523 </change_format>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	524 </data>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	525 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	526
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	527 <xml name="output_save_matrix_values">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	528 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	529 <filter>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	530 ((
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	531 output['showOutputSettings'] == 'yes' and
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	532 output['saveMatrix'] is True
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	533 ))
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	534 </filter>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	535 </data>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	536 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	537
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	538 <xml name="output_graphic_outputs">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	539 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	540 <filter>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	541 ((
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	542 output['showOutputSettings'] == 'yes' and
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	543 output['saveData'] is True
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	544 ))
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	545 </filter>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	546 </data>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	547 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	548 <filter>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	549 ((
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	550 output['showOutputSettings'] == 'yes' and
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	551 output['saveSortedRegions'] is True
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	552 ))
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	553 </filter>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	554 </data>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	555 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	556
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	557 <xml name="track_input_h5_macro">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	558 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	559 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	560 <xml name="track_input_bed_macro">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	561 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	562 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	563 <xml name="track_input_bedgraph_macro">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	564 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	565 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	566 <xml name="track_input_bigwig_macro">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	567 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	568 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	569 <xml name="track_input_bedgraph_matrix_macro">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	570 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	571 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	572 <xml name="track_input_tabular_macro">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	573 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	574 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	575 <xml name="plot_title">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	576 <param name="title" type="text" optional="true" label="Plot title"/>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	577 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	578
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	579 <xml name="spacer_macro">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	580 <param name="spacer_width" type="float" value="" optional="True"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	581 label="Include spacer at the end of the track." help="Width of the spacer." />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	582 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	583 <xml name="fontsize_macro">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	584 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	585 </xml>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 bgruening parents: diff changeset	586 </macros>

Mercurial > repos > bgruening > hicexplorer_hicaggregatecontacts

annotate macros.xml @ 1:ec59bf4c3d06 draft