hicexplorer_hicmergematrixbins: macros.xml annotate

author	iuc
date	Fri, 27 Apr 2018 05:52:42 -0400 (2018-04-27)
parents	d444ca8616f5
children	f2dd8dd02a95

rev	line source
0 f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	1 <macros>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
7 d444ca8616f5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 6 diff changeset	3 <token name="@WRAPPER_VERSION@">2.1.2</token>
6 0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	4 <token name="@USE_RANGE@">
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	5 #if $use_range.select_use_range == "yes_use_range":
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	6 --range $range_min:$range_max
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	7 #end if
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	8 </token>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	9
0 f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	10 <xml name="requirements">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	11 <requirements>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	13 <yield />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	14 </requirements>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	15 <version_command>@BINARY@ --version</version_command>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	16 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	17
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	18 <xml name="citations">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	19 <citations>
4 936741507eb1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058 iuc parents: 3 diff changeset	20 <citation type="doi">10.5281/zenodo.1133705</citation>
0 f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	21 <yield />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	22 </citations>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	23 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	24
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	25 <xml name="zMax">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	26 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	27 </xml>
6 0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	28 <xml name="use_range">
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	29 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
7 d444ca8616f5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 6 diff changeset	30 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
6 0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	31 <option value="no_use_range">No restriction</option>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	32 <option value="yes_use_range">Only consider counts within a range</option>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	33 </param>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	34 <when value="no_use_range"/>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	35 <when value="yes_use_range">
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	36 <expand macro='range' />
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	37 </when>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	38 </conditional>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	39 </xml>
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	40
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	41 <xml name="range">
7 d444ca8616f5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 6 diff changeset	42 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
d444ca8616f5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 6 diff changeset	43 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
6 0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	44 </xml>
0 f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	45
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	46 <xml name="colormap">
2 62e0b9817f77 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04 iuc parents: 1 diff changeset	47 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
0 f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	48 <option value="RdYlBu">RdYlBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	49 <option value="Accent">Accent</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	50 <option value="Spectral">Spectral</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	51 <option value="Set1">Set1</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	52 <option value="Set2">Set2</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	53 <option value="Set3">Set3</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	54 <option value="Dark2">Dark2</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	55 <option value="Reds">Reds</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	56 <option value="Oranges">Oranges</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	57 <option value="Greens">Greens</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	58 <option value="Blues">Blues</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	59 <option value="Greys">Greys</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	60 <option value="Purples">Purples</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	61 <option value="Paired">Paired</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	62 <option value="Pastel1">Pastel1</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	63 <option value="Pastel2">Pastel2</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	64 <option value="spring">spring</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	65 <option value="summer">summer</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	66 <option value="autumn">autumn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	67 <option value="winter">winter</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	68 <option value="hot">hot</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	69 <option value="coolwarm">coolwarm</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	70 <option value="cool">cool</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	71 <option value="seismic">seismic</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	72 <option value="terrain">terrain</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	73 <option value="ocean">ocean</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	74 <option value="rainbow">rainbow</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	75 <option value="bone">bone</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	76 <option value="flag">flag</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	77 <option value="prism">prism</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	78 <option value="cubehelix">cubehelix</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	79 <option value="binary">binary</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	80 <option value="pink">pink</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	81 <option value="gray">gray</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	82 <option value="copper">copper</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	83 <option value="BrBG">BrBG</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	84 <option value="BuGn">BuGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	85 <option value="BuPu">BuPu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	86 <option value="GnBu">GnBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	87 <option value="OrRd">OrRd</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	88 <option value="PiYG">PiYG</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	89 <option value="PRGn">PRGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	90 <option value="PuOr">PuOr</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	91 <option value="PuRd">PuRd</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	92 <option value="PuBu">PuBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	93 <option value="RdBu">RdBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	94 <option value="RdGy">RdGy</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	95 <option value="RdPu">RdPu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	96 <option value="YlGn">YlGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	97 <option value="PuBuGn">PuBuGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	98 <option value="RdYlGn">RdYlGn</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	99 <option value="YlGnBu">YlGnBu</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	100 <option value="YlOrBr">YlOrBr</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	101 <option value="YlOrRd">YlOrRd</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	102 <option value="gist_gray">gist_gray</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	103 <option value="gist_stern">gist_stern</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	104 <option value="gist_earth">gist_earth</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	105 <option value="gist_yarg">gist_yarg</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	106 <option value="gist_ncar">gist_ncar</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	107 <option value="gist_rainbow">gist_rainbow</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	108 <option value="gist_heat">gist_heat</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	109 <option value="gnuplot">gnuplot</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	110 <option value="gnuplot2">gnuplot2</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	111 <option value="CMRmap">CMRmap</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	112 <option value="bwr">bwr</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	113 <option value="hsv">hsv</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	114 <option value="brg">brg</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	115 <option value="jet">jet</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	116 <option value="afmhot">afmhot</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	117 <option value="Accent_r">Accent reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	118 <option value="Spectral_r">Spectral reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	119 <option value="Set1_r">Set1 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	120 <option value="Set2_r">Set2 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	121 <option value="Set3_r">Set3 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	122 <option value="Dark2_r">Dark2 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	123 <option value="Reds_r">Reds reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	124 <option value="Oranges_r">Oranges reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	125 <option value="Greens_r">Greens reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	126 <option value="Blues_r">Blues reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	127 <option value="Greys_r">Greys reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	128 <option value="Purples_r">Purples reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	129 <option value="Paired_r">Paired reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	130 <option value="Pastel1_r">Pastel1 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	131 <option value="Pastel2_r">Pastel2 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	132 <option value="spring_r">spring reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	133 <option value="summer_r">summer reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	134 <option value="autumn_r">autumn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	135 <option value="winter_r">winter reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	136 <option value="hot_r">hot reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	137 <option value="coolwarm_r">coolwarm reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	138 <option value="cool_r">cool reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	139 <option value="seismic_r">seismic reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	140 <option value="terrain_r">terrain reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	141 <option value="ocean_r">ocean reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	142 <option value="rainbow_r">rainbow reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	143 <option value="bone_r">bone reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	144 <option value="flag_r">flag reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	145 <option value="prism_r">prism reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	146 <option value="cubehelix_r">cubehelix reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	147 <option value="binary_r">binary reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	148 <option value="pink_r">pink reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	149 <option value="gray_r">gray reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	150 <option value="copper_r">copper reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	151 <option value="BrBG_r">BrBG reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	152 <option value="BuGn_r">BuGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	153 <option value="BuPu_r">BuPu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	154 <option value="GnBu_r">GnBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	155 <option value="OrRd_r">OrRd reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	156 <option value="PiYG_r">PiYG reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	157 <option value="PRGn_r">PRGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	158 <option value="PuOr_r">PuOr reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	159 <option value="PuRd_r">PuRd reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	160 <option value="PuBu_r">PuBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	161 <option value="RdBu_r">RdBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	162 <option value="RdGy_r">RdGy reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	163 <option value="RdPu_r">RdPu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	164 <option value="YlGn_r">YlGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	165 <option value="PuBuGn_r">PuBuGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	167 <option value="RdYlGn_r">RdYlGn reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	168 <option value="YlGnBu_r">YlGnBu reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	169 <option value="YlOrBr_r">YlOrBr reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	170 <option value="YlOrRd_r">YlOrRd reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	171 <option value="gist_gray_r">gist_gray reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	172 <option value="gist_stern_r">gist_stern reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	173 <option value="gist_earth_r">gist_earth reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	174 <option value="gist_yarg_r">gist_yarg reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	175 <option value="gist_ncar_r">gist_ncar reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	176 <option value="gist_rainbow_r">gist_rainbow reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	177 <option value="gist_heat_r">gist_heat reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	178 <option value="gnuplot_r">gnuplot reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	179 <option value="gnuplot2_r">gnuplot2 reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	180 <option value="CMRmap_r">CMRmap reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	181 <option value="bwr_r">bwr reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	182 <option value="hsv_r">hsv reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	183 <option value="brg_r">brg reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	184 <option value="jet_r">jet reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	185 <option value="afmhot_r">afmhot reversed</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	186 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	187 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	188
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	189
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	190 <xml name="multiple_input_matrices">
7 d444ca8616f5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 6 diff changeset	191 <repeat name="input_files" title="Hi-C Matrix files" min="2">
3 2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 2 diff changeset	192 <param name="matrix" type="data" format="h5,cool"
7 d444ca8616f5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 6 diff changeset	193 label="Hi-C Matrix file"
0 f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	194 help=""/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	195 <param name="mlabel" type="text" size="30" optional="true" value=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	196 label="Label"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	197 help="Label to use in the output. If not given the dataset name will be used instead."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	198 </repeat>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	199 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	200
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	201 <token name="@multiple_input_matrices@">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	202 #set $matrices = []
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	203 #set $mlabels = []
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	204 #for $counter, $i in enumerate($input_files):
3 2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 2 diff changeset	205 ln -s $i.matrix #echo str($counter)+'_matrix'#;
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 2 diff changeset	206 #silent $matrices.append( '%s_matrix' % $counter )
0 f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	207
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	208 #if str($i.mlabel.value) != "":
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	210 #else
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	211 #set $mlabels += ['"%s"' % ($i.matrix.name)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	212 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	213 #end for
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	214 #set $mlabels = ' '.join($mlabels)
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	215 #set $matrices = ' '.join($matrices)
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	216 </token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	217
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	218
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	219 <xml name="region">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	220 <param name="region" type="text" label="Region of the genome to limit the operation"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	222 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	223
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	224
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	225
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	226 <xml name="kmeans_clustering">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	227 <conditional name="used_multiple_regions">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	228 <param name="used_multiple_regions_options" type="select"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	229 label="Did you compute the matrix with more than one groups of regions?"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	230 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	231 <option value="yes">Yes, I used multiple groups of regions</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	232 <option value="no">No, I used only one group</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	233 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	234 <when value="no">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	235 <conditional name="clustering">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	236 <param name="clustering_options" type="select" label="Clustering algorithm">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	237 <option value="none">No clustering</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	238 <option value="kmeans">Kmeans clustering</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	239 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	240 <when value="kmeans">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	242 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	243 </when>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	244 <when value="none" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	245 </conditional>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	246 </when>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	247 <when value="yes" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	248 </conditional>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	249 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	250
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	251 <token name="@KMEANS_CLUSTERING@">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	256 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	257 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	258 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	259 </token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	260
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	261 <xml name="samFlag">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	262 <param name="samFlag" type="integer" optional="true" value=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	263 label="Filter reads based on the SAM flag"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	264 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	265 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	266 <xml name="plotNumbers">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	268 label="Plot the correlation value"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	270 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	271 <xml name="doNotExtendPairedEnds">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	273 label="Do not extend paired ends"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	274 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	275 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	276
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	277 <xml name="ignoreDuplicates">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	279 label="Ignore duplicates"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	280 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	281 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	282
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	283 <xml name="minMappingQuality">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	285 label="Minimum mapping quality"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	286 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	287 Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	288 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	289 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	290
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	291 <xml name="skipZeros">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	293 label ="Skip zeros"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	294 help ="If set, then zero counts that happen for all BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	295 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	296
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	297 <xml name="fragmentLength">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	298 <param name="fragmentLength" type="integer" value="300" min="1"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	299 label="Fragment length used for the sequencing"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	301 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	302
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	303 <xml name="scaleFactor">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	306 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	307
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	308 <xml name="xMax">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	309 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	310 label="Max value for the x-axis in counts per bin" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	311 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	312
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	313 <xml name="filterThreshold">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	315 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	316
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	319 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	320
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	321
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	322 <xml name="pseudocount">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	323 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	324 </xml>
3 2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 2 diff changeset	325 <xml name='matrix_h5_cooler_macro'>
6 0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	326 <param name='matrix_h5_cooler' type="data" format="h5,cool"
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	327 label="Matrix to compute on"/>
3 2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 2 diff changeset	328 </xml>
2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 2 diff changeset	329 <xml name='matrix_h5_cooler_multiple_macro'>
6 0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	330 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 4 diff changeset	331 label="Matricies to compute on" multiple="true"/>
3 2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 2 diff changeset	332 </xml>
0 f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	333 <token name="@REFERENCES@">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	334
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	335 .. class:: infomark
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	336
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	337 For more information on the tools, please visit our `help site`_.
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	338
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	339 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	340
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	341 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	342
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	343 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	344 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	345 .. _help site: https://hicexplorer.readthedocs.org
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	346
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	347 </token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	348
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	349
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	350 <xml name="multiple_input_bams">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	351 <repeat name="input_files" title="BAM files" min="2">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	352 <param name="bamfile" type="data" format="bam"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	353 label="Bam file"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	354 help="The BAM file must be sorted."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	355 <param name="label" type="text" size="30" optional="true" value=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	356 label="Label"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	357 help="Label to use in the output. If not given the dataset name will be used instead."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	358 </repeat>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	359 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	360
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	361 <xml name="multiple_input_bigwigs">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	362 <repeat name="input_files" title="BigWig files" min="2">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	363 <param name="bigwigfile" type="data" format="bigwig"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	364 label="Bigwig file"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	365 help="The Bigwig file must be sorted."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	366 <param name="label" type="text" size="30" optional="true" value=""
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	367 label="Label"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	368 help="Label to use in the output. If not given the dataset name will be used instead."/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	369 </repeat>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	370 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	371
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	372 <xml name="plotTitle">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	373 <param name="plotTitle" type="text" value="" size="30" optional="True"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	374 label="Title of the plot"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	375 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	376 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	377
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	378 <token name="@multiple_input_bams@">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	379 #import tempfile
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	380 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	381 #set files=[]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	382 #set labels=[]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	383 #for $i in $input_files:
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	385 #set $temp_input_path = $temp_input_handle.name
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	386 #silent $temp_input_handle.close()
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	387 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	388 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	389 #silent $files.append('%s.bam' % $temp_input_path)
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	390
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	391 ##set $files += [str($i.bamfile)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	392 #if str($i.label.value) != "":
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	393 #set $labels += ["\"%s\"" % ($i.label.value)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	394 #else
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	395 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	396 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	397 #end for
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	398 </token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	399
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	400 <token name="@multiple_input_bigwigs@">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	401 #import tempfile
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	402 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	403 #set files=[]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	404 #set labels=[]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	405 #for $i in $input_files:
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	406 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	407 #set $temp_input_path = $temp_input_handle.name
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	408 #silent $temp_input_handle.close()
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	409 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	410 #silent $files.append('%s.bw' % $temp_input_path)
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	411
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	412 ##set $files += [str($i.bigwigfile)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	413 #if str($i.label.value) != "":
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	414 #set $labels += ["\"%s\"" % ($i.label.value)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	415 #else
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	416 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	417 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	418 #end for
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	419 </token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	420
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	421 <xml name="reference_genome_source">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	422 <conditional name="source">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	423 <param name="ref_source" type="select" label="Reference genome">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	424 <option value="cached">locally cached</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	425 <option value="history">in your history</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	426 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	427 <when value="cached">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	428 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	429 <options from_data_table="deepTools_seqs">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	430 <filter type="sort_by" column="1" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	431 <validator type="no_options" message="No indexes are available." />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	432 </options>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	433 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	434 </when>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	435 <when value="history">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	436 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	437 </when>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	438 </conditional>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	439 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	440
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	441 <token name="@reference_genome_source@">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	442 #if $source.ref_source=="history":
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	443 --genome $source.input1
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	444 #else:
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	445 --genome "${source.input1_2bit.fields.path}"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	446 #end if
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	447 </token>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	448
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	449 <xml name="effectiveGenomeSize">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	450 <conditional name="effectiveGenomeSize">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	451 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	452 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	453 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	454 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	455 <option value="93260000">ce10 (93260000)</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	456 <option value="121400000">dm3 (121400000)</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	457 <option value="2451960000" selected="true">hg19 (2451960000)</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	458 <option value="2150570000">mm9 (2150570000)</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	459 <option value="specific">user specified</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	460 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	461 <when value="specific">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	462 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	463 </when>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	464 <when value="2150570000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	465 <when value="2451960000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	466 <when value="121400000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	467 <when value="93260000" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	468 </conditional>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	469 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	470
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	471 <xml name="image_file_format">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	472 <param name="outFileFormat" type="select" label="Image file format">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	473 <option value="png" selected="true">png</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	474 <option value="pdf">pdf</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	475 <option value="svg">svg</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	476 <option value="eps">eps</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	477 <option value="emf">emf</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	478 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	479 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	480
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	481 <xml name="missingDataAsZero">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	482 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	483 label ="Treat missing data as zero"
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	484 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	485 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	486
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	487 <xml name="input_save_matrix_values">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	488 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	489 </xml>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	490
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	491 <xml name="input_graphic_output_settings">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	492 <conditional name="output" >
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	493 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	494 <option value="no" selected="true">no</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	495 <option value="yes">yes</option>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	496 </param>
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	497 <when value="no" />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	498 <when value="yes">
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	499 <yield />
f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: diff changeset	500 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>

0

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1 <macros>

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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>

7

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3 <token name="@WRAPPER_VERSION@">2.1.2</token>

6

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4 <token name="@USE_RANGE@">

0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d

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5 #if $use_range.select_use_range == "yes_use_range":

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6 --range $range_min:$range_max

0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d

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7 #end if

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8 </token>

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9

0

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10 <xml name="requirements">

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11 <requirements>

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12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>

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13 <yield />

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14 </requirements>

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15 <version_command>@BINARY@ --version</version_command>

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16 </xml>

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17

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18 <xml name="citations">

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19 <citations>

4

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20 <citation type="doi">10.5281/zenodo.1133705</citation>

0

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21 <yield />

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22 </citations>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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23 </xml>

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24

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25 <xml name="zMax">

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26 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/>

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27 </xml>

6

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28 <xml name="use_range">

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29 <conditional name="use_range">

7

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30 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">

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31 <option value="no_use_range">No restriction</option>

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32 <option value="yes_use_range">Only consider counts within a range</option>

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33 </param>

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34 <when value="no_use_range"/>

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35 <when value="yes_use_range">

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36 <expand macro='range' />

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37 </when>

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38 </conditional>

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39 </xml>

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40

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41 <xml name="range">

7

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42 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>

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43 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>

6

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44 </xml>

0

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45

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46 <xml name="colormap">

2

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47 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">

0

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48 <option value="RdYlBu">RdYlBu</option>

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49 <option value="Accent">Accent</option>

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50 <option value="Spectral">Spectral</option>

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51 <option value="Set1">Set1</option>

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52 <option value="Set2">Set2</option>

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53 <option value="Set3">Set3</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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54 <option value="Dark2">Dark2</option>

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55 <option value="Reds">Reds</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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56 <option value="Oranges">Oranges</option>

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57 <option value="Greens">Greens</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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58 <option value="Blues">Blues</option>

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59 <option value="Greys">Greys</option>

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60 <option value="Purples">Purples</option>

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61 <option value="Paired">Paired</option>

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62 <option value="Pastel1">Pastel1</option>

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63 <option value="Pastel2">Pastel2</option>

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64 <option value="spring">spring</option>

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65 <option value="summer">summer</option>

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66 <option value="autumn">autumn</option>

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67 <option value="winter">winter</option>

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68 <option value="hot">hot</option>

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69 <option value="coolwarm">coolwarm</option>

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70 <option value="cool">cool</option>

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71 <option value="seismic">seismic</option>

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72 <option value="terrain">terrain</option>

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73 <option value="ocean">ocean</option>

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74 <option value="rainbow">rainbow</option>

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75 <option value="bone">bone</option>

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76 <option value="flag">flag</option>

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77 <option value="prism">prism</option>

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78 <option value="cubehelix">cubehelix</option>

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79 <option value="binary">binary</option>

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80 <option value="pink">pink</option>

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81 <option value="gray">gray</option>

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82 <option value="copper">copper</option>

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83 <option value="BrBG">BrBG</option>

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84 <option value="BuGn">BuGn</option>

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85 <option value="BuPu">BuPu</option>

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86 <option value="GnBu">GnBu</option>

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87 <option value="OrRd">OrRd</option>

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88 <option value="PiYG">PiYG</option>

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89 <option value="PRGn">PRGn</option>

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90 <option value="PuOr">PuOr</option>

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91 <option value="PuRd">PuRd</option>

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92 <option value="PuBu">PuBu</option>

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93 <option value="RdBu">RdBu</option>

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94 <option value="RdGy">RdGy</option>

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95 <option value="RdPu">RdPu</option>

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96 <option value="YlGn">YlGn</option>

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97 <option value="PuBuGn">PuBuGn</option>

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98 <option value="RdYlGn">RdYlGn</option>

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99 <option value="YlGnBu">YlGnBu</option>

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100 <option value="YlOrBr">YlOrBr</option>

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101 <option value="YlOrRd">YlOrRd</option>

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102 <option value="gist_gray">gist_gray</option>

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103 <option value="gist_stern">gist_stern</option>

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104 <option value="gist_earth">gist_earth</option>

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105 <option value="gist_yarg">gist_yarg</option>

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106 <option value="gist_ncar">gist_ncar</option>

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107 <option value="gist_rainbow">gist_rainbow</option>

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108 <option value="gist_heat">gist_heat</option>

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109 <option value="gnuplot">gnuplot</option>

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110 <option value="gnuplot2">gnuplot2</option>

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111 <option value="CMRmap">CMRmap</option>

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112 <option value="bwr">bwr</option>

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113 <option value="hsv">hsv</option>

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114 <option value="brg">brg</option>

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115 <option value="jet">jet</option>

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116 <option value="afmhot">afmhot</option>

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117 <option value="Accent_r">Accent reversed</option>

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118 <option value="Spectral_r">Spectral reversed</option>

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119 <option value="Set1_r">Set1 reversed</option>

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120 <option value="Set2_r">Set2 reversed</option>

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121 <option value="Set3_r">Set3 reversed</option>

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122 <option value="Dark2_r">Dark2 reversed</option>

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123 <option value="Reds_r">Reds reversed</option>

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124 <option value="Oranges_r">Oranges reversed</option>

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125 <option value="Greens_r">Greens reversed</option>

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126 <option value="Blues_r">Blues reversed</option>

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127 <option value="Greys_r">Greys reversed</option>

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128 <option value="Purples_r">Purples reversed</option>

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129 <option value="Paired_r">Paired reversed</option>

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130 <option value="Pastel1_r">Pastel1 reversed</option>

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131 <option value="Pastel2_r">Pastel2 reversed</option>

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132 <option value="spring_r">spring reversed</option>

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133 <option value="summer_r">summer reversed</option>

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134 <option value="autumn_r">autumn reversed</option>

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135 <option value="winter_r">winter reversed</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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136 <option value="hot_r">hot reversed</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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137 <option value="coolwarm_r">coolwarm reversed</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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138 <option value="cool_r">cool reversed</option>

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139 <option value="seismic_r">seismic reversed</option>

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140 <option value="terrain_r">terrain reversed</option>

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141 <option value="ocean_r">ocean reversed</option>

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142 <option value="rainbow_r">rainbow reversed</option>

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143 <option value="bone_r">bone reversed</option>

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144 <option value="flag_r">flag reversed</option>

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145 <option value="prism_r">prism reversed</option>

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146 <option value="cubehelix_r">cubehelix reversed</option>

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147 <option value="binary_r">binary reversed</option>

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148 <option value="pink_r">pink reversed</option>

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149 <option value="gray_r">gray reversed</option>

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150 <option value="copper_r">copper reversed</option>

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151 <option value="BrBG_r">BrBG reversed</option>

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152 <option value="BuGn_r">BuGn reversed</option>

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153 <option value="BuPu_r">BuPu reversed</option>

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154 <option value="GnBu_r">GnBu reversed</option>

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155 <option value="OrRd_r">OrRd reversed</option>

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156 <option value="PiYG_r">PiYG reversed</option>

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157 <option value="PRGn_r">PRGn reversed</option>

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158 <option value="PuOr_r">PuOr reversed</option>

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159 <option value="PuRd_r">PuRd reversed</option>

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160 <option value="PuBu_r">PuBu reversed</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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161 <option value="RdBu_r">RdBu reversed</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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162 <option value="RdGy_r">RdGy reversed</option>

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163 <option value="RdPu_r">RdPu reversed</option>

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164 <option value="YlGn_r">YlGn reversed</option>

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165 <option value="PuBuGn_r">PuBuGn reversed</option>

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166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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167 <option value="RdYlGn_r">RdYlGn reversed</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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168 <option value="YlGnBu_r">YlGnBu reversed</option>

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169 <option value="YlOrBr_r">YlOrBr reversed</option>

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170 <option value="YlOrRd_r">YlOrRd reversed</option>

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171 <option value="gist_gray_r">gist_gray reversed</option>

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172 <option value="gist_stern_r">gist_stern reversed</option>

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173 <option value="gist_earth_r">gist_earth reversed</option>

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174 <option value="gist_yarg_r">gist_yarg reversed</option>

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175 <option value="gist_ncar_r">gist_ncar reversed</option>

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176 <option value="gist_rainbow_r">gist_rainbow reversed</option>

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177 <option value="gist_heat_r">gist_heat reversed</option>

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178 <option value="gnuplot_r">gnuplot reversed</option>

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179 <option value="gnuplot2_r">gnuplot2 reversed</option>

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180 <option value="CMRmap_r">CMRmap reversed</option>

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181 <option value="bwr_r">bwr reversed</option>

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182 <option value="hsv_r">hsv reversed</option>

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183 <option value="brg_r">brg reversed</option>

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184 <option value="jet_r">jet reversed</option>

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185 <option value="afmhot_r">afmhot reversed</option>

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186 </param>

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187 </xml>

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188

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189

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190 <xml name="multiple_input_matrices">

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191 <repeat name="input_files" title="Hi-C Matrix files" min="2">

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192 <param name="matrix" type="data" format="h5,cool"

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193 label="Hi-C Matrix file"

0

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194 help=""/>

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195 <param name="mlabel" type="text" size="30" optional="true" value=""

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196 label="Label"

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197 help="Label to use in the output. If not given the dataset name will be used instead."/>

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198 </repeat>

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199 </xml>

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200

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201 <token name="@multiple_input_matrices@">

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202 #set $matrices = []

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203 #set $mlabels = []

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204 #for $counter, $i in enumerate($input_files):

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205 ln -s $i.matrix #echo str($counter)+'_matrix'#;

2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

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206 #silent $matrices.append( '%s_matrix' % $counter )

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207

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208 #if str($i.mlabel.value) != "":

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209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]

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210 #else

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211 #set $mlabels += ['"%s"' % ($i.matrix.name)]

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212 #end if

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213 #end for

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214 #set $mlabels = ' '.join($mlabels)

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215 #set $matrices = ' '.join($matrices)

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216 </token>

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217

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218

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219 <xml name="region">

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220 <param name="region" type="text" label="Region of the genome to limit the operation"

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221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>

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222 </xml>

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223

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224

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225

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226 <xml name="kmeans_clustering">

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227 <conditional name="used_multiple_regions">

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228 <param name="used_multiple_regions_options" type="select"

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229 label="Did you compute the matrix with more than one groups of regions?"

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230 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">

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231 <option value="yes">Yes, I used multiple groups of regions</option>

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232 <option value="no">No, I used only one group</option>

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233 </param>

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234 <when value="no">

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235 <conditional name="clustering">

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236 <param name="clustering_options" type="select" label="Clustering algorithm">

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237 <option value="none">No clustering</option>

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238 <option value="kmeans">Kmeans clustering</option>

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239 </param>

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240 <when value="kmeans">

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241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"

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242 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>

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243 </when>

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244 <when value="none" />

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245 </conditional>

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246 </when>

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247 <when value="yes" />

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248 </conditional>

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249 </xml>

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250

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251 <token name="@KMEANS_CLUSTERING@">

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252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':

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253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':

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254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:

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255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans

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256 #end if

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257 #end if

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258 #end if

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259 </token>

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260

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261 <xml name="samFlag">

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262 <param name="samFlag" type="integer" optional="true" value=""

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263 label="Filter reads based on the SAM flag"

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264 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>

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265 </xml>

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266 <xml name="plotNumbers">

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267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""

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268 label="Plot the correlation value"

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269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>

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270 </xml>

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271 <xml name="doNotExtendPairedEnds">

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272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""

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273 label="Do not extend paired ends"

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274 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>

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275 </xml>

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276

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277 <xml name="ignoreDuplicates">

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278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""

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279 label="Ignore duplicates"

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280 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />

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281 </xml>

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282

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283 <xml name="minMappingQuality">

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284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"

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285 label="Minimum mapping quality"

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286 help= "If set, only reads that have a mapping quality score higher than the given value are considered.

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287 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.

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288 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>

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289 </xml>

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290

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291 <xml name="skipZeros">

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292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""

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293 label ="Skip zeros"

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294 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />

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295 </xml>

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296

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297 <xml name="fragmentLength">

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298 <param name="fragmentLength" type="integer" value="300" min="1"

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299 label="Fragment length used for the sequencing"

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300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>

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301 </xml>

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302

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303 <xml name="scaleFactor">

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304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>

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305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>

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306 </xml>

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307

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308 <xml name="xMax">

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309 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""

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310 label="Max value for the x-axis in counts per bin" />

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311 </xml>

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312

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313 <xml name="filterThreshold">

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314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"

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315 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>

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316

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317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"

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318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>

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319 </xml>

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320

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321

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322 <xml name="pseudocount">

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323 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>

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324 </xml>

3

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325 <xml name='matrix_h5_cooler_macro'>

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326 <param name='matrix_h5_cooler' type="data" format="h5,cool"

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327 label="Matrix to compute on"/>

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328 </xml>

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329 <xml name='matrix_h5_cooler_multiple_macro'>

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330 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"

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331 label="Matricies to compute on" multiple="true"/>

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332 </xml>

0

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333 <token name="@REFERENCES@">

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334

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335 .. class:: infomark

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336

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337 For more information on the tools, please visit our `help site`_.

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338

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339 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com

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340

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341 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.

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342

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343 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/

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344 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de

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345 .. _help site: https://hicexplorer.readthedocs.org

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346

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347 </token>

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348

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349

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350 <xml name="multiple_input_bams">

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351 <repeat name="input_files" title="BAM files" min="2">

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352 <param name="bamfile" type="data" format="bam"

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353 label="Bam file"

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354 help="The BAM file must be sorted."/>

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355 <param name="label" type="text" size="30" optional="true" value=""

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356 label="Label"

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357 help="Label to use in the output. If not given the dataset name will be used instead."/>

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358 </repeat>

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359 </xml>

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360

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361 <xml name="multiple_input_bigwigs">

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362 <repeat name="input_files" title="BigWig files" min="2">

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363 <param name="bigwigfile" type="data" format="bigwig"

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364 label="Bigwig file"

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365 help="The Bigwig file must be sorted."/>

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366 <param name="label" type="text" size="30" optional="true" value=""

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367 label="Label"

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368 help="Label to use in the output. If not given the dataset name will be used instead."/>

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369 </repeat>

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370 </xml>

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371

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372 <xml name="plotTitle">

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373 <param name="plotTitle" type="text" value="" size="30" optional="True"

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374 label="Title of the plot"

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375 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />

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376 </xml>

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377

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378 <token name="@multiple_input_bams@">

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379 #import tempfile

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380 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())

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381 #set files=[]

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382 #set labels=[]

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383 #for $i in $input_files:

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384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )

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385 #set $temp_input_path = $temp_input_handle.name

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386 #silent $temp_input_handle.close()

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387 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))

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388 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))

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389 #silent $files.append('%s.bam' % $temp_input_path)

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390

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391 ##set $files += [str($i.bamfile)]

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392 #if str($i.label.value) != "":

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393 #set $labels += ["\"%s\"" % ($i.label.value)]

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394 #else

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395 #set $labels += ["\"%s\"" % ($i.bamfile.name)]

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396 #end if

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397 #end for

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398 </token>

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399

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400 <token name="@multiple_input_bigwigs@">

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401 #import tempfile

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402 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())

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403 #set files=[]

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404 #set labels=[]

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405 #for $i in $input_files:

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406 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )

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407 #set $temp_input_path = $temp_input_handle.name

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408 #silent $temp_input_handle.close()

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409 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))

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410 #silent $files.append('%s.bw' % $temp_input_path)

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411

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412 ##set $files += [str($i.bigwigfile)]

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413 #if str($i.label.value) != "":

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414 #set $labels += ["\"%s\"" % ($i.label.value)]

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415 #else

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416 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]

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417 #end if

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418 #end for

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419 </token>

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420

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421 <xml name="reference_genome_source">

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422 <conditional name="source">

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423 <param name="ref_source" type="select" label="Reference genome">

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424 <option value="cached">locally cached</option>

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425 <option value="history">in your history</option>

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426 </param>

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427 <when value="cached">

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428 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">

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429 <options from_data_table="deepTools_seqs">

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430 <filter type="sort_by" column="1" />

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431 <validator type="no_options" message="No indexes are available." />

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432 </options>

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433 </param>

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434 </when>

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435 <when value="history">

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436 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />

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437 </when>

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438 </conditional>

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439 </xml>

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440

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441 <token name="@reference_genome_source@">

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442 #if $source.ref_source=="history":

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443 --genome $source.input1

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444 #else:

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445 --genome "${source.input1_2bit.fields.path}"

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446 #end if

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447 </token>

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448

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449 <xml name="effectiveGenomeSize">

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450 <conditional name="effectiveGenomeSize">

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451 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"

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452 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.

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453 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.

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454 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">

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455 <option value="93260000">ce10 (93260000)</option>

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456 <option value="121400000">dm3 (121400000)</option>

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457 <option value="2451960000" selected="true">hg19 (2451960000)</option>

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458 <option value="2150570000">mm9 (2150570000)</option>

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459 <option value="specific">user specified</option>

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460 </param>

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461 <when value="specific">

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462 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>

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463 </when>

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464 <when value="2150570000" />

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465 <when value="2451960000" />

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466 <when value="121400000" />

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467 <when value="93260000" />

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468 </conditional>

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469 </xml>

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470

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471 <xml name="image_file_format">

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472 <param name="outFileFormat" type="select" label="Image file format">

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473 <option value="png" selected="true">png</option>

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474 <option value="pdf">pdf</option>

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475 <option value="svg">svg</option>

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476 <option value="eps">eps</option>

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477 <option value="emf">emf</option>

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478 </param>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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479 </xml>

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480

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481 <xml name="missingDataAsZero">

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482 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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483 label ="Treat missing data as zero"

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484 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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485 </xml>

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486

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487 <xml name="input_save_matrix_values">

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488 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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489 </xml>

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490

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491 <xml name="input_graphic_output_settings">

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492 <conditional name="output" >

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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493 <param name="showOutputSettings" type="select" label="Show advanced output settings" >

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494 <option value="no" selected="true">no</option>

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495 <option value="yes">yes</option>

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496 </param>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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497 <when value="no" />

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498 <when value="yes">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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499 <yield />

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500 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>

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501 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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502 </when>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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503 </conditional>

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504 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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505

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506 <xml name="input_image_file_format">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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507 <param name="outFileFormat" type="select" label="Image file format">

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508 <option value="png" selected="true">png</option>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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509 <option value="pdf">pdf</option>

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510 <option value="svg">svg</option>

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511 <option value="eps">eps</option>

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512 <option value="emf">emf</option>

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513 </param>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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514 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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515

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516 <xml name="output_image_file_format">

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517 <data format="png" name="outFileName" label="${tool.name} image">

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518 <change_format>

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519 <when input="output.outFileFormat" value="pdf" format="pdf" />

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520 <when input="output.outFileFormat" value="svg" format="svg" />

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521 <when input="output.outFileFormat" value="eps" format="eps" />

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522 <when input="output.outFileFormat" value="emf" format="emf" />

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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523 </change_format>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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524 </data>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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525 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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526

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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527 <xml name="output_save_matrix_values">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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528 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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529 <filter>

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530 ((

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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531 output['showOutputSettings'] == 'yes' and

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532 output['saveMatrix'] is True

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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533 ))

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534 </filter>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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535 </data>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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536 </xml>

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537

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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538 <xml name="output_graphic_outputs">

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539 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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540 <filter>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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541 ((

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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542 output['showOutputSettings'] == 'yes' and

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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543 output['saveData'] is True

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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544 ))

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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545 </filter>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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546 </data>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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547 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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548 <filter>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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549 ((

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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550 output['showOutputSettings'] == 'yes' and

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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551 output['saveSortedRegions'] is True

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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552 ))

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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553 </filter>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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554 </data>

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555 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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556

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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557 <xml name="track_input_h5_macro">

3

2a62d67cab68 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

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558 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>

0

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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559 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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560 <xml name="track_input_bed_macro">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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561 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>

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562 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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563 <xml name="track_input_bedgraph_macro">

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564 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>

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565 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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566 <xml name="track_input_bigwig_macro">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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567 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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568 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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569 <xml name="track_input_bedgraph_matrix_macro">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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570 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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571 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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572 <xml name="track_input_tabular_macro">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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573 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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574 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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575 <xml name="plot_title">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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576 <param name="title" type="text" optional="true" label="Plot title"/>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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577 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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578

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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579 <xml name="spacer_macro">

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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580 <param name="spacer_width" type="float" value="" optional="True"

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0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d

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581 label="Include spacer at the end of the track." help="Width of the spacer." />

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f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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582 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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583 <xml name="fontsize_macro">

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0c6d98e9c6e8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d

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584 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />

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f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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585 </xml>

f2b51d398496 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

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586 </macros>

Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

annotate macros.xml @ 8:2259773f21cc draft