hicexplorer_hicfindtads: macros.xml annotate

annotate macros.xml @ 1:72883c28fdcd draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f

author	bgruening
date	Mon, 03 Apr 2017 07:29:57 -0400
parents	aab371aa615e
children	a9c1d76b90c4

rev	line source
0 aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	1 <macros>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	2 <xml name="stdio">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	3 <stdio>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	4 <exit_code range="1:" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	5 <exit_code range=":-1" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	6 <regex match="Error:" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	7 <regex match="Exception:" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	8 <regex match="EXception:" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	9 <regex match="Traceback" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	10 </stdio>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	11 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	12
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	13 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
1 72883c28fdcd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f bgruening parents: 0 diff changeset	14 <token name="@WRAPPER_VERSION@">1.7.2</token>
0 aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	15 <xml name="requirements">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	16 <requirements>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	17 <requirement type="package" version="2.7.13">python</requirement>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	18 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	19 <yield />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	20 </requirements>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	21 <expand macro="stdio" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	22 <version_command>@BINARY@ --version</version_command>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	23 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	24
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	25 <xml name="citations">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	26 <citations>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	27 <citation type="doi">10.5281/zenodo.159780</citation>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	28 <yield />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	29 </citations>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	30 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	31
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	32 <xml name="zMax">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	33 <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 -->
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	34 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	35
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	36 <xml name="colormap">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	37 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	38 <option value="RdYlBu">RdYlBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	39 <option value="Accent">Accent</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	40 <option value="Spectral">Spectral</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	41 <option value="Set1">Set1</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	42 <option value="Set2">Set2</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	43 <option value="Set3">Set3</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	44 <option value="Dark2">Dark2</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	45 <option value="Reds">Reds</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	46 <option value="Oranges">Oranges</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	47 <option value="Greens">Greens</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	48 <option value="Blues">Blues</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	49 <option value="Greys">Greys</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	50 <option value="Purples">Purples</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	51 <option value="Paired">Paired</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	52 <option value="Pastel1">Pastel1</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	53 <option value="Pastel2">Pastel2</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	54 <option value="spring">spring</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	55 <option value="summer">summer</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	56 <option value="autumn">autumn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	57 <option value="winter">winter</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	58 <option value="hot">hot</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	59 <option value="coolwarm">coolwarm</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	60 <option value="cool">cool</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	61 <option value="seismic">seismic</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	62 <option value="terrain">terrain</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	63 <option value="ocean">ocean</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	64 <option value="rainbow">rainbow</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	65 <option value="bone">bone</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	66 <option value="flag">flag</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	67 <option value="prism">prism</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	68 <option value="cubehelix">cubehelix</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	69 <option value="binary">binary</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	70 <option value="pink">pink</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	71 <option value="gray">gray</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	72 <option value="copper">copper</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	73 <option value="BrBG">BrBG</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	74 <option value="BuGn">BuGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	75 <option value="BuPu">BuPu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	76 <option value="GnBu">GnBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	77 <option value="OrRd">OrRd</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	78 <option value="PiYG">PiYG</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	79 <option value="PRGn">PRGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	80 <option value="PuOr">PuOr</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	81 <option value="PuRd">PuRd</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	82 <option value="PuBu">PuBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	83 <option value="RdBu">RdBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	84 <option value="RdGy">RdGy</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	85 <option value="RdPu">RdPu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	86 <option value="YlGn">YlGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	87 <option value="PuBuGn">PuBuGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	88 <option value="RdYlGn">RdYlGn</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	89 <option value="YlGnBu">YlGnBu</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	90 <option value="YlOrBr">YlOrBr</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	91 <option value="YlOrRd">YlOrRd</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	92 <option value="gist_gray">gist_gray</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	93 <option value="gist_stern">gist_stern</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	94 <option value="gist_earth">gist_earth</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	95 <option value="gist_yarg">gist_yarg</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	96 <option value="gist_ncar">gist_ncar</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	97 <option value="gist_rainbow">gist_rainbow</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	98 <option value="gist_heat">gist_heat</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	99 <option value="gnuplot">gnuplot</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	100 <option value="gnuplot2">gnuplot2</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	101 <option value="CMRmap">CMRmap</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	102 <option value="bwr">bwr</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	103 <option value="hsv">hsv</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	104 <option value="brg">brg</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	105 <option value="jet">jet</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	106 <option value="afmhot">afmhot</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	107 <option value="Accent_r">Accent reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	108 <option value="Spectral_r">Spectral reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	109 <option value="Set1_r">Set1 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	110 <option value="Set2_r">Set2 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	111 <option value="Set3_r">Set3 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	112 <option value="Dark2_r">Dark2 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	113 <option value="Reds_r">Reds reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	114 <option value="Oranges_r">Oranges reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	115 <option value="Greens_r">Greens reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	116 <option value="Blues_r">Blues reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	117 <option value="Greys_r">Greys reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	118 <option value="Purples_r">Purples reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	119 <option value="Paired_r">Paired reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	120 <option value="Pastel1_r">Pastel1 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	121 <option value="Pastel2_r">Pastel2 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	122 <option value="spring_r">spring reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	123 <option value="summer_r">summer reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	124 <option value="autumn_r">autumn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	125 <option value="winter_r">winter reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	126 <option value="hot_r">hot reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	127 <option value="coolwarm_r">coolwarm reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	128 <option value="cool_r">cool reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	129 <option value="seismic_r">seismic reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	130 <option value="terrain_r">terrain reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	131 <option value="ocean_r">ocean reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	132 <option value="rainbow_r">rainbow reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	133 <option value="bone_r">bone reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	134 <option value="flag_r">flag reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	135 <option value="prism_r">prism reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	136 <option value="cubehelix_r">cubehelix reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	137 <option value="binary_r">binary reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	138 <option value="pink_r">pink reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	139 <option value="gray_r">gray reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	140 <option value="copper_r">copper reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	141 <option value="BrBG_r">BrBG reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	142 <option value="BuGn_r">BuGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	143 <option value="BuPu_r">BuPu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	144 <option value="GnBu_r">GnBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	145 <option value="OrRd_r">OrRd reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	146 <option value="PiYG_r">PiYG reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	147 <option value="PRGn_r">PRGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	148 <option value="PuOr_r">PuOr reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	149 <option value="PuRd_r">PuRd reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	150 <option value="PuBu_r">PuBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	151 <option value="RdBu_r">RdBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	152 <option value="RdGy_r">RdGy reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	153 <option value="RdPu_r">RdPu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	154 <option value="YlGn_r">YlGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	155 <option value="PuBuGn_r">PuBuGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	156 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	157 <option value="RdYlGn_r">RdYlGn reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	158 <option value="YlGnBu_r">YlGnBu reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	159 <option value="YlOrBr_r">YlOrBr reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	160 <option value="YlOrRd_r">YlOrRd reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	161 <option value="gist_gray_r">gist_gray reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	162 <option value="gist_stern_r">gist_stern reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	163 <option value="gist_earth_r">gist_earth reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	164 <option value="gist_yarg_r">gist_yarg reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	165 <option value="gist_ncar_r">gist_ncar reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	166 <option value="gist_rainbow_r">gist_rainbow reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	167 <option value="gist_heat_r">gist_heat reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	168 <option value="gnuplot_r">gnuplot reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	169 <option value="gnuplot2_r">gnuplot2 reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	170 <option value="CMRmap_r">CMRmap reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	171 <option value="bwr_r">bwr reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	172 <option value="hsv_r">hsv reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	173 <option value="brg_r">brg reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	174 <option value="jet_r">jet reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	175 <option value="afmhot_r">afmhot reversed</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	176 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	177 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	178
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	179
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	180 <xml name="multiple_input_matrices">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	181 <repeat name="input_files" title="HiC Matrix files" min="2">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	182 <param name="matrix" type="data" format="h5"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	183 label="HiC Matrix file"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	184 help=""/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	185 <param name="mlabel" type="text" size="30" optional="true" value=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	186 label="Label"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	187 help="Label to use in the output. If not given the dataset name will be used instead."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	188 </repeat>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	189 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	190
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	191 <token name="@multiple_input_matrices@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	192 #set $matrices = []
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	193 #set $mlabels = []
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	194 #for $counter, $i in enumerate($input_files):
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	195 ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	196 #silent $matrices.append( '%s.npz.h5' % $counter )
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	197
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	198 #if str($i.mlabel.value) != "":
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	199 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	200 #else
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	201 #set $mlabels += ['"%s"' % ($i.matrix.name)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	202 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	203 #end for
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	204 #set $mlabels = ' '.join($mlabels)
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	205 #set $matrices = ' '.join($matrices)
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	206 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	207
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	208
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	209 <xml name="region">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	210 <param name="region" type="text" label="Region of the genome to limit the operation"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	211 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	212 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	213
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	214
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	215
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	216 <xml name="kmeans_clustering">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	217 <conditional name="used_multiple_regions">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	218 <param name="used_multiple_regions_options" type="select"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	219 label="Did you compute the matrix with more than one groups of regions?"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	220 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.">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	221 <option value="yes">Yes, I used multiple groups of regions</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	222 <option value="no">No, I used only one group</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	223 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	224 <when value="no">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	225 <conditional name="clustering">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	226 <param name="clustering_options" type="select" label="Clustering algorithm">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	227 <option value="none">No clustering</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	228 <option value="kmeans">Kmeans clustering</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	229 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	230 <when value="kmeans">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	231 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	232 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)."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	233 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	234 <when value="none" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	235 </conditional>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	236 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	237 <when value="yes" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	238 </conditional>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	239 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	240
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	241 <token name="@KMEANS_CLUSTERING@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	242 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	243 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	244 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	245 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	246 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	247 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	248 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	249 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	250
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	251 <xml name="samFlag">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	252 <param name="samFlag" type="integer" optional="true" value=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	253 label="Filter reads based on the SAM flag"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	254 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)"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	255 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	256 <xml name="plotNumbers">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	257 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	258 label="Plot the correlation value"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	259 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	260 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	261 <xml name="doNotExtendPairedEnds">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	262 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	263 label="Do not extend paired ends"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	264 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)"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	265 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	266
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	267 <xml name="ignoreDuplicates">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	268 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	269 label="Ignore duplicates"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	270 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)" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	271 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	272
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	273 <xml name="minMappingQuality">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	274 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	275 label="Minimum mapping quality"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	276 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	277 Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	278 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."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	279 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	280
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	281 <xml name="skipZeros">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	282 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	283 label ="Skip zeros"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	284 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)" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	285 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	286
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	287 <xml name="fragmentLength">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	288 <param name="fragmentLength" type="integer" value="300" min="1"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	289 label="Fragment length used for the sequencing"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	290 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	291 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	292
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	293 <xml name="scaleFactor">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	294 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	295 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	296 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	297
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	298 <xml name="xMax">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	299 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	300 label="Max value for the x-axis in counts per bin" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	301 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	302
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	303 <xml name="filterThreshold">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	304 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	305 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	306
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	307 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	308 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	309 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	310
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	311
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	312 <xml name="pseudocount">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	313 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	314 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	315
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	316 <token name="@REFERENCES@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	317
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	318 .. class:: infomark
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	319
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	320 For more information on the tools, please visit our `help site`_.
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	321
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	322 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	323
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	324 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	325
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	326 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	327 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	328 .. _help site: https://github.com/fidelram/deepTools/wiki/
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	329
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	330 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	331
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	332
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	333 <xml name="multiple_input_bams">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	334 <repeat name="input_files" title="BAM files" min="2">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	335 <param name="bamfile" type="data" format="bam"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	336 label="Bam file"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	337 help="The BAM file must be sorted."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	338 <param name="label" type="text" size="30" optional="true" value=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	339 label="Label"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	340 help="Label to use in the output. If not given the dataset name will be used instead."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	341 </repeat>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	342 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	343
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	344 <xml name="multiple_input_bigwigs">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	345 <repeat name="input_files" title="BigWig files" min="2">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	346 <param name="bigwigfile" type="data" format="bigwig"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	347 label="Bigwig file"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	348 help="The Bigwig file must be sorted."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	349 <param name="label" type="text" size="30" optional="true" value=""
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	350 label="Label"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	351 help="Label to use in the output. If not given the dataset name will be used instead."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	352 </repeat>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	353 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	354
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	355 <xml name="plotTitle">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	356 <param name="plotTitle" type="text" value="" size="30" optional="True"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	357 label="Title of the plot"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	358 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	359 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	360
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	361 <token name="@multiple_input_bams@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	362 #import tempfile
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	363 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	364 #set files=[]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	365 #set labels=[]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	366 #for $i in $input_files:
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	367 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	368 #set $temp_input_path = $temp_input_handle.name
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	369 #silent $temp_input_handle.close()
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	370 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	371 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	372 #silent $files.append('%s.bam' % $temp_input_path)
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	373
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	374 ##set $files += [str($i.bamfile)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	375 #if str($i.label.value) != "":
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	376 #set $labels += ["\"%s\"" % ($i.label.value)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	377 #else
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	378 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	379 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	380 #end for
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	381 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	382
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	383 <token name="@multiple_input_bigwigs@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	384 #import tempfile
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	385 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	386 #set files=[]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	387 #set labels=[]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	388 #for $i in $input_files:
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	389 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	390 #set $temp_input_path = $temp_input_handle.name
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	391 #silent $temp_input_handle.close()
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	392 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	393 #silent $files.append('%s.bw' % $temp_input_path)
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	394
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	395 ##set $files += [str($i.bigwigfile)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	396 #if str($i.label.value) != "":
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	397 #set $labels += ["\"%s\"" % ($i.label.value)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	398 #else
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	399 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	400 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	401 #end for
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	402 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	403
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	404 <xml name="reference_genome_source">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	405 <conditional name="source">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	406 <param name="ref_source" type="select" label="Reference genome">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	407 <option value="cached">locally cached</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	408 <option value="history">in your history</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	409 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	410 <when value="cached">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	411 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	412 <options from_data_table="deepTools_seqs">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	413 <filter type="sort_by" column="1" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	414 <validator type="no_options" message="No indexes are available." />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	415 </options>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	416 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	417 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	418 <when value="history">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	419 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	420 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	421 </conditional>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	422 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	423
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	424 <token name="@reference_genome_source@">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	425 #if $source.ref_source=="history":
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	426 --genome $source.input1
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	427 #else:
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	428 --genome "${source.input1_2bit.fields.path}"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	429 #end if
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	430 </token>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	431
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	432 <xml name="effectiveGenomeSize">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	433 <conditional name="effectiveGenomeSize">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	434 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	435 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.
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	436 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	437 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	438 <option value="93260000">ce10 (93260000)</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	439 <option value="121400000">dm3 (121400000)</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	440 <option value="2451960000" selected="true">hg19 (2451960000)</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	441 <option value="2150570000">mm9 (2150570000)</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	442 <option value="specific">user specified</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	443 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	444 <when value="specific">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	445 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	446 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	447 <when value="2150570000" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	448 <when value="2451960000" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	449 <when value="121400000" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	450 <when value="93260000" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	451 </conditional>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	452 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	453
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	454 <xml name="image_file_format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	455 <param name="outFileFormat" type="select" label="Image file format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	456 <option value="png" selected="true">png</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	457 <option value="pdf">pdf</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	458 <option value="svg">svg</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	459 <option value="eps">eps</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	460 <option value="emf">emf</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	461 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	462 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	463
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	464 <xml name="missingDataAsZero">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	465 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	466 label ="Treat missing data as zero"
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	467 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." />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	468 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	469
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	470 <xml name="input_save_matrix_values">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	471 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	472 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	473
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	474 <xml name="input_graphic_output_settings">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	475 <conditional name="output" >
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	476 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	477 <option value="no" selected="true">no</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	478 <option value="yes">yes</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	479 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	480 <when value="no" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	481 <when value="yes">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	482 <yield />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	483 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	484 <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."/>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	485 </when>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	486 </conditional>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	487 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	488
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	489 <xml name="input_image_file_format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	490 <param name="outFileFormat" type="select" label="Image file format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	491 <option value="png" selected="true">png</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	492 <option value="pdf">pdf</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	493 <option value="svg">svg</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	494 <option value="eps">eps</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	495 <option value="emf">emf</option>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	496 </param>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	497 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	498
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	499 <xml name="output_image_file_format">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	500 <data format="png" name="outFileName" label="${tool.name} image">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	501 <change_format>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	502 <when input="output.outFileFormat" value="pdf" format="pdf" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	503 <when input="output.outFileFormat" value="svg" format="svg" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	504 <when input="output.outFileFormat" value="eps" format="eps" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	505 <when input="output.outFileFormat" value="emf" format="emf" />
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	506 </change_format>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	507 </data>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	508 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	509
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	510 <xml name="output_save_matrix_values">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	511 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	512 <filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	513 ((
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	514 output['showOutputSettings'] == 'yes' and
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	515 output['saveMatrix'] is True
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	516 ))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	517 </filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	518 </data>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	519 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	520
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	521 <xml name="output_graphic_outputs">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	522 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	523 <filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	524 ((
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	525 output['showOutputSettings'] == 'yes' and
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	526 output['saveData'] is True
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	527 ))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	528 </filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	529 </data>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	530 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	531 <filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	532 ((
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	533 output['showOutputSettings'] == 'yes' and
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	534 output['saveSortedRegions'] is True
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	535 ))
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	536 </filter>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	537 </data>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	538 </xml>
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	539
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	540
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	541
aab371aa615e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	542 </macros>

Mercurial > repos > bgruening > hicexplorer_hicfindtads

annotate macros.xml @ 1:72883c28fdcd draft