hicexplorer_hiccorrelate: macros.xml annotate

annotate macros.xml @ 0:1b41da63ef0a draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty

author	bgruening
date	Sun, 09 Oct 2016 17:35:58 -0400
parents
children	3fc885f53423

rev	line source
0 1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	1 <macros>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	2 <xml name="stdio">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	3 <stdio>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	4 <exit_code range="1:" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	5 <exit_code range=":-1" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	6 <regex match="Error:" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	7 <regex match="Exception:" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	8 <regex match="EXception:" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	9 <regex match="Traceback" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	10 </stdio>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	11 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	12
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	13 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	14 <token name="@WRAPPER_VERSION@">1.2</token>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	15 <xml name="requirements">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	16 <requirements>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	17 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	18 <yield />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	19 </requirements>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	20 <expand macro="stdio" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	21 <version_command>@BINARY@ --version</version_command>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	22 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	23
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	24 <xml name="citations">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	25 <citations>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	26 <citation type="doi">10.5281/zenodo.159780</citation>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	27 <yield />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	28 </citations>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	29 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	30
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	31 <xml name="zMax">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	32 <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 -->
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	33 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	34
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	35 <xml name="colormap">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	36 <param argument="--colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	37 <option value="RdYlBu" selected="true">RdYlBu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	38 <option value="Accent">Accent</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	39 <option value="Spectral">Spectral</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	40 <option value="Set1">Set1</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	41 <option value="Set2">Set2</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	42 <option value="Set3">Set3</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	43 <option value="Dark2">Dark2</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	44 <option value="Reds">Reds</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	45 <option value="Oranges">Oranges</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	46 <option value="Greens">Greens</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	47 <option value="Blues">Blues</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	48 <option value="Greys">Greys</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	49 <option value="Purples">Purples</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	50 <option value="Paired">Paired</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	51 <option value="Pastel1">Pastel1</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	52 <option value="Pastel2">Pastel2</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	53 <option value="spring">spring</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	54 <option value="summer">summer</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	55 <option value="autumn">autumn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	56 <option value="winter">winter</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	57 <option value="hot">hot</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	58 <option value="coolwarm">coolwarm</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	59 <option value="cool">cool</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	60 <option value="seismic">seismic</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	61 <option value="terrain">terrain</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	62 <option value="ocean">ocean</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	63 <option value="rainbow">rainbow</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	64 <option value="bone">bone</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	65 <option value="flag">flag</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	66 <option value="prism">prism</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	67 <option value="cubehelix">cubehelix</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	68 <option value="binary">binary</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	69 <option value="pink">pink</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	70 <option value="gray">gray</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	71 <option value="copper">copper</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	72 <option value="BrBG">BrBG</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	73 <option value="BuGn">BuGn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	74 <option value="BuPu">BuPu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	75 <option value="GnBu">GnBu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	76 <option value="OrRd">OrRd</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	77 <option value="PiYG">PiYG</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	78 <option value="PRGn">PRGn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	79 <option value="PuOr">PuOr</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	80 <option value="PuRd">PuRd</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	81 <option value="PuBu">PuBu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	82 <option value="RdBu">RdBu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	83 <option value="RdGy">RdGy</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	84 <option value="RdPu">RdPu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	85 <option value="YlGn">YlGn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	86 <option value="PuBuGn">PuBuGn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	87 <option value="RdYlGn">RdYlGn</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	88 <option value="YlGnBu">YlGnBu</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	89 <option value="YlOrBr">YlOrBr</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	90 <option value="YlOrRd">YlOrRd</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	91 <option value="gist_gray">gist_gray</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	92 <option value="gist_stern">gist_stern</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	93 <option value="gist_earth">gist_earth</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	94 <option value="gist_yarg">gist_yarg</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	95 <option value="gist_ncar">gist_ncar</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	96 <option value="gist_rainbow">gist_rainbow</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	97 <option value="gist_heat">gist_heat</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	98 <option value="gnuplot">gnuplot</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	99 <option value="gnuplot2">gnuplot2</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	100 <option value="CMRmap">CMRmap</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	101 <option value="bwr">bwr</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	102 <option value="hsv">hsv</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	103 <option value="brg">brg</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	104 <option value="jet">jet</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	105 <option value="afmhot">afmhot</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	106 <option value="Accent_r">Accent reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	107 <option value="Spectral_r">Spectral reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	108 <option value="Set1_r">Set1 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	109 <option value="Set2_r">Set2 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	110 <option value="Set3_r">Set3 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	111 <option value="Dark2_r">Dark2 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	112 <option value="Reds_r">Reds reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	113 <option value="Oranges_r">Oranges reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	114 <option value="Greens_r">Greens reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	115 <option value="Blues_r">Blues reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	116 <option value="Greys_r">Greys reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	117 <option value="Purples_r">Purples reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	118 <option value="Paired_r">Paired reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	119 <option value="Pastel1_r">Pastel1 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	120 <option value="Pastel2_r">Pastel2 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	121 <option value="spring_r">spring reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	122 <option value="summer_r">summer reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	123 <option value="autumn_r">autumn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	124 <option value="winter_r">winter reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	125 <option value="hot_r">hot reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	126 <option value="coolwarm_r">coolwarm reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	127 <option value="cool_r">cool reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	128 <option value="seismic_r">seismic reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	129 <option value="terrain_r">terrain reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	130 <option value="ocean_r">ocean reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	131 <option value="rainbow_r">rainbow reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	132 <option value="bone_r">bone reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	133 <option value="flag_r">flag reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	134 <option value="prism_r">prism reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	135 <option value="cubehelix_r">cubehelix reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	136 <option value="binary_r">binary reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	137 <option value="pink_r">pink reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	138 <option value="gray_r">gray reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	139 <option value="copper_r">copper reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	140 <option value="BrBG_r">BrBG reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	141 <option value="BuGn_r">BuGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	142 <option value="BuPu_r">BuPu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	143 <option value="GnBu_r">GnBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	144 <option value="OrRd_r">OrRd reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	145 <option value="PiYG_r">PiYG reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	146 <option value="PRGn_r">PRGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	147 <option value="PuOr_r">PuOr reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	148 <option value="PuRd_r">PuRd reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	149 <option value="PuBu_r">PuBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	150 <option value="RdBu_r">RdBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	151 <option value="RdGy_r">RdGy reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	152 <option value="RdPu_r">RdPu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	153 <option value="YlGn_r">YlGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	154 <option value="PuBuGn_r">PuBuGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	155 <option value="RdYlBu_r">RdYlBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	156 <option value="RdYlGn_r">RdYlGn reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	157 <option value="YlGnBu_r">YlGnBu reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	158 <option value="YlOrBr_r">YlOrBr reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	159 <option value="YlOrRd_r">YlOrRd reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	160 <option value="gist_gray_r">gist_gray reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	161 <option value="gist_stern_r">gist_stern reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	162 <option value="gist_earth_r">gist_earth reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	163 <option value="gist_yarg_r">gist_yarg reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	164 <option value="gist_ncar_r">gist_ncar reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	165 <option value="gist_rainbow_r">gist_rainbow reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	166 <option value="gist_heat_r">gist_heat reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	167 <option value="gnuplot_r">gnuplot reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	168 <option value="gnuplot2_r">gnuplot2 reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	169 <option value="CMRmap_r">CMRmap reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	170 <option value="bwr_r">bwr reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	171 <option value="hsv_r">hsv reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	172 <option value="brg_r">brg reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	173 <option value="jet_r">jet reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	174 <option value="afmhot_r">afmhot reversed</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	175 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	176 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	177
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	178
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	179 <xml name="multiple_input_matrices">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	180 <repeat name="input_files" title="HiC Matrix files" min="2">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	181 <param name="matrix" type="data" format="h5"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	182 label="HiC Matrix file"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	183 help=""/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	184 <param name="mlabel" type="text" size="30" optional="true" value=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	185 label="Label"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	186 help="Label to use in the output. If not given the dataset name will be used instead."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	187 </repeat>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	188 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	189
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	190 <token name="@multiple_input_matrices@">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	191 #set $matrices = []
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	192 #set $mlabels = []
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	193 #for $counter, $i in enumerate($input_files):
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	194 ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	195 #silent $matrices.append( '%s.npz.h5' % $counter )
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	196
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	197 #if str($i.mlabel.value) != "":
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	198 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	199 #else
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	200 #set $mlabels += ['"%s"' % ($i.matrix.name)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	201 #end if
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	202 #end for
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	203 #set $mlabels = ' '.join($mlabels)
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	204 #set $matrices = ' '.join($matrices)
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	205 </token>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	206
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	207
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	208 <xml name="region">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	209 <param name="region" type="text" label="Region of the genome to limit the operation"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	210 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	211 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	212
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	213
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	214
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	215 <xml name="kmeans_clustering">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	216 <conditional name="used_multiple_regions">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	217 <param name="used_multiple_regions_options" type="select"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	218 label="Did you compute the matrix with more than one groups of regions?"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	219 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.">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	220 <option value="yes">Yes, I used multiple groups of regions</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	221 <option value="no">No, I used only one group</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	222 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	223 <when value="no">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	224 <conditional name="clustering">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	225 <param name="clustering_options" type="select" label="Clustering algorithm">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	226 <option value="none">No clustering</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	227 <option value="kmeans">Kmeans clustering</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	228 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	229 <when value="kmeans">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	230 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	231 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)."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	232 </when>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	233 <when value="none" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	234 </conditional>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	235 </when>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	236 <when value="yes" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	237 </conditional>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	238 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	239
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	240 <token name="@KMEANS_CLUSTERING@">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	241 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	242 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	243 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	244 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	245 #end if
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	246 #end if
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	247 #end if
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	248 </token>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	249
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	250 <xml name="samFlag">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	251 <param name="samFlag" type="integer" optional="true" value=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	252 label="Filter reads based on the SAM flag"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	253 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)"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	254 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	255 <xml name="plotNumbers">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	256 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	257 label="Plot the correlation value"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	258 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	259 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	260 <xml name="doNotExtendPairedEnds">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	261 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	262 label="Do not extend paired ends"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	263 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)"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	264 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	265
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	266 <xml name="ignoreDuplicates">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	267 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	268 label="Ignore duplicates"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	269 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)" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	270 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	271
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	272 <xml name="minMappingQuality">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	273 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	274 label="Minimum mapping quality"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	275 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	276 Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	277 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."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	278 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	279
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	280 <xml name="skipZeros">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	281 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	282 label ="Skip zeros"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	283 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)" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	284 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	285
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	286 <xml name="fragmentLength">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	287 <param name="fragmentLength" type="integer" value="300" min="1"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	288 label="Fragment length used for the sequencing"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	289 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	290 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	291
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	292 <xml name="scaleFactor">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	293 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	294 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	295 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	296
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	297 <xml name="xMax">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	298 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	299 label="Max value for the x-axis in counts per bin" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	300 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	301
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	302 <xml name="filterThreshold">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	303 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	304 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	305
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	306 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	307 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	308 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	309
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	310
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	311 <xml name="pseudocount">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	312 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	313 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	314
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	315 <token name="@REFERENCES@">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	316
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	317 .. class:: infomark
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	318
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	319 For more information on the tools, please visit our `help site`_.
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	320
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	321 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	322
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	323 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	324
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	325 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	326 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	327 .. _help site: https://github.com/fidelram/deepTools/wiki/
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	328
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	329 </token>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	330
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	331
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	332 <xml name="multiple_input_bams">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	333 <repeat name="input_files" title="BAM files" min="2">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	334 <param name="bamfile" type="data" format="bam"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	335 label="Bam file"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	336 help="The BAM file must be sorted."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	337 <param name="label" type="text" size="30" optional="true" value=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	338 label="Label"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	339 help="Label to use in the output. If not given the dataset name will be used instead."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	340 </repeat>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	341 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	342
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	343 <xml name="multiple_input_bigwigs">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	344 <repeat name="input_files" title="BigWig files" min="2">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	345 <param name="bigwigfile" type="data" format="bigwig"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	346 label="Bigwig file"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	347 help="The Bigwig file must be sorted."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	348 <param name="label" type="text" size="30" optional="true" value=""
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	349 label="Label"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	350 help="Label to use in the output. If not given the dataset name will be used instead."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	351 </repeat>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	352 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	353
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	354 <xml name="plotTitle">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	355 <param name="plotTitle" type="text" value="" size="30" optional="True"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	356 label="Title of the plot"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	357 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	358 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	359
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	360 <token name="@multiple_input_bams@">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	361 #import tempfile
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	362 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	363 #set files=[]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	364 #set labels=[]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	365 #for $i in $input_files:
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	366 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	367 #set $temp_input_path = $temp_input_handle.name
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	368 #silent $temp_input_handle.close()
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	369 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	370 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	371 #silent $files.append('%s.bam' % $temp_input_path)
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	372
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	373 ##set $files += [str($i.bamfile)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	374 #if str($i.label.value) != "":
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	375 #set $labels += ["\"%s\"" % ($i.label.value)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	376 #else
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	377 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	378 #end if
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	379 #end for
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	380 </token>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	381
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	382 <token name="@multiple_input_bigwigs@">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	383 #import tempfile
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	384 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	385 #set files=[]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	386 #set labels=[]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	387 #for $i in $input_files:
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	388 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	389 #set $temp_input_path = $temp_input_handle.name
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	390 #silent $temp_input_handle.close()
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	391 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	392 #silent $files.append('%s.bw' % $temp_input_path)
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	393
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	394 ##set $files += [str($i.bigwigfile)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	395 #if str($i.label.value) != "":
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	396 #set $labels += ["\"%s\"" % ($i.label.value)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	397 #else
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	398 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	399 #end if
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	400 #end for
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	401 </token>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	402
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	403 <xml name="reference_genome_source">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	404 <conditional name="source">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	405 <param name="ref_source" type="select" label="Reference genome">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	406 <option value="cached">locally cached</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	407 <option value="history">in your history</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	408 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	409 <when value="cached">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	410 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	411 <options from_data_table="deepTools_seqs">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	412 <filter type="sort_by" column="1" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	413 <validator type="no_options" message="No indexes are available." />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	414 </options>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	415 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	416 </when>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	417 <when value="history">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	418 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	419 </when>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	420 </conditional>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	421 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	422
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	423 <token name="@reference_genome_source@">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	424 #if $source.ref_source=="history":
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	425 --genome $source.input1
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	426 #else:
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	427 --genome "${source.input1_2bit.fields.path}"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	428 #end if
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	429 </token>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	430
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	431 <xml name="effectiveGenomeSize">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	432 <conditional name="effectiveGenomeSize">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	433 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	434 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.
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	435 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	436 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.">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	437 <option value="93260000">ce10 (93260000)</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	438 <option value="121400000">dm3 (121400000)</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	439 <option value="2451960000" selected="true">hg19 (2451960000)</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	440 <option value="2150570000">mm9 (2150570000)</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	441 <option value="specific">user specified</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	442 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	443 <when value="specific">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	444 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	445 </when>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	446 <when value="2150570000" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	447 <when value="2451960000" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	448 <when value="121400000" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	449 <when value="93260000" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	450 </conditional>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	451 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	452
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	453 <xml name="image_file_format">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	454 <param name="outFileFormat" type="select" label="Image file format">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	455 <option value="png" selected="true">png</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	456 <option value="pdf">pdf</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	457 <option value="svg">svg</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	458 <option value="eps">eps</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	459 <option value="emf">emf</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	460 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	461 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	462
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	463 <xml name="missingDataAsZero">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	464 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	465 label ="Treat missing data as zero"
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	466 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." />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	467 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	468
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	469 <xml name="input_save_matrix_values">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	470 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	471 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	472
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	473 <xml name="input_graphic_output_settings">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	474 <conditional name="output" >
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	475 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	476 <option value="no" selected="true">no</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	477 <option value="yes">yes</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	478 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	479 <when value="no" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	480 <when value="yes">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	481 <yield />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	482 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	483 <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."/>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	484 </when>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	485 </conditional>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	486 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	487
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	488 <xml name="input_image_file_format">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	489 <param name="outFileFormat" type="select" label="Image file format">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	490 <option value="png" selected="true">png</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	491 <option value="pdf">pdf</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	492 <option value="svg">svg</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	493 <option value="eps">eps</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	494 <option value="emf">emf</option>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	495 </param>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	496 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	497
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	498 <xml name="output_image_file_format">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	499 <data format="png" name="outFileName" label="${tool.name} image">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	500 <change_format>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	501 <when input="output.outFileFormat" value="pdf" format="pdf" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	502 <when input="output.outFileFormat" value="svg" format="svg" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	503 <when input="output.outFileFormat" value="eps" format="eps" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	504 <when input="output.outFileFormat" value="emf" format="emf" />
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	505 </change_format>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	506 </data>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	507 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	508
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	509 <xml name="output_save_matrix_values">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	510 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	511 <filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	512 ((
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	513 output['showOutputSettings'] == 'yes' and
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	514 output['saveMatrix'] is True
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	515 ))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	516 </filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	517 </data>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	518 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	519
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	520 <xml name="output_graphic_outputs">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	521 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	522 <filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	523 ((
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	524 output['showOutputSettings'] == 'yes' and
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	525 output['saveData'] is True
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	526 ))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	527 </filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	528 </data>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	529 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	530 <filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	531 ((
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	532 output['showOutputSettings'] == 'yes' and
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	533 output['saveSortedRegions'] is True
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	534 ))
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	535 </filter>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	536 </data>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	537 </xml>
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	538
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	539
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	540
1b41da63ef0a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	541 </macros>

Mercurial > repos > bgruening > hicexplorer_hiccorrelate

annotate macros.xml @ 0:1b41da63ef0a draft