hicexplorer_hicsummatrices: macros.xml annotate

annotate macros.xml @ 10:551510b684b7 draft

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

author	iuc
date	Fri, 27 Apr 2018 03:19:28 -0400
parents	673c3280e576
children	2f18082f828b

rev	line source
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	1 <macros>
3 81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
10 551510b684b7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	3 <token name="@WRAPPER_VERSION@">2.1.2</token>
9 673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	4 <token name="@USE_RANGE@">
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	5 #if $use_range.select_use_range == "yes_use_range":
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	6 --range $range_min:$range_max
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	7 #end if
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	8 </token>
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	9
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	10 <xml name="requirements">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	11 <requirements>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	13 <yield />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	14 </requirements>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	15 <version_command>@BINARY@ --version</version_command>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	16 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	17
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	18 <xml name="citations">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	19 <citations>
7 b712d550c29a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058 iuc parents: 6 diff changeset	20 <citation type="doi">10.5281/zenodo.1133705</citation>
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	21 <yield />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	22 </citations>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	23 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	24
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	25 <xml name="zMax">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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 -->
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	27 </xml>
9 673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	28 <xml name="use_range">
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	29 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
10 551510b684b7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 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.">
9 673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	31 <option value="no_use_range">No restriction</option>
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	32 <option value="yes_use_range">Only consider counts within a range</option>
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	33 </param>
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	34 <when value="no_use_range"/>
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	35 <when value="yes_use_range">
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	36 <expand macro='range' />
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	37 </when>
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	38 </conditional>
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	39 </xml>
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	40
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	41 <xml name="range">
10 551510b684b7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 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."/>
551510b684b7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	43 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
9 673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	44 </xml>
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	45
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	46 <xml name="colormap">
5 01803c0d5952 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04 iuc parents: 4 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">
1 a6ccec9faaa3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: 0 diff changeset	48 <option value="RdYlBu">RdYlBu</option>
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	49 <option value="Accent">Accent</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	50 <option value="Spectral">Spectral</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	51 <option value="Set1">Set1</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	52 <option value="Set2">Set2</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	53 <option value="Set3">Set3</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	54 <option value="Dark2">Dark2</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	55 <option value="Reds">Reds</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	56 <option value="Oranges">Oranges</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	57 <option value="Greens">Greens</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	58 <option value="Blues">Blues</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	59 <option value="Greys">Greys</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	60 <option value="Purples">Purples</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	61 <option value="Paired">Paired</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	62 <option value="Pastel1">Pastel1</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	63 <option value="Pastel2">Pastel2</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	64 <option value="spring">spring</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	65 <option value="summer">summer</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	66 <option value="autumn">autumn</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	67 <option value="winter">winter</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	68 <option value="hot">hot</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	69 <option value="coolwarm">coolwarm</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	70 <option value="cool">cool</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	71 <option value="seismic">seismic</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	72 <option value="terrain">terrain</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	73 <option value="ocean">ocean</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	74 <option value="rainbow">rainbow</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	75 <option value="bone">bone</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	76 <option value="flag">flag</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	77 <option value="prism">prism</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	78 <option value="cubehelix">cubehelix</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	79 <option value="binary">binary</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	80 <option value="pink">pink</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	81 <option value="gray">gray</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	82 <option value="copper">copper</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	83 <option value="BrBG">BrBG</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	84 <option value="BuGn">BuGn</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	85 <option value="BuPu">BuPu</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	86 <option value="GnBu">GnBu</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	87 <option value="OrRd">OrRd</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	88 <option value="PiYG">PiYG</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	89 <option value="PRGn">PRGn</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	90 <option value="PuOr">PuOr</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	91 <option value="PuRd">PuRd</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	92 <option value="PuBu">PuBu</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	93 <option value="RdBu">RdBu</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	94 <option value="RdGy">RdGy</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	95 <option value="RdPu">RdPu</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	96 <option value="YlGn">YlGn</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	97 <option value="PuBuGn">PuBuGn</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	98 <option value="RdYlGn">RdYlGn</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	99 <option value="YlGnBu">YlGnBu</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	100 <option value="YlOrBr">YlOrBr</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	101 <option value="YlOrRd">YlOrRd</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	102 <option value="gist_gray">gist_gray</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	103 <option value="gist_stern">gist_stern</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	104 <option value="gist_earth">gist_earth</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	105 <option value="gist_yarg">gist_yarg</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	106 <option value="gist_ncar">gist_ncar</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	107 <option value="gist_rainbow">gist_rainbow</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	108 <option value="gist_heat">gist_heat</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	109 <option value="gnuplot">gnuplot</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	110 <option value="gnuplot2">gnuplot2</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	111 <option value="CMRmap">CMRmap</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	112 <option value="bwr">bwr</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	113 <option value="hsv">hsv</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	114 <option value="brg">brg</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	115 <option value="jet">jet</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	116 <option value="afmhot">afmhot</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	117 <option value="Accent_r">Accent reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	118 <option value="Spectral_r">Spectral reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	119 <option value="Set1_r">Set1 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	120 <option value="Set2_r">Set2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	121 <option value="Set3_r">Set3 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	122 <option value="Dark2_r">Dark2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	123 <option value="Reds_r">Reds reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	124 <option value="Oranges_r">Oranges reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	125 <option value="Greens_r">Greens reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	126 <option value="Blues_r">Blues reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	127 <option value="Greys_r">Greys reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	128 <option value="Purples_r">Purples reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	129 <option value="Paired_r">Paired reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	130 <option value="Pastel1_r">Pastel1 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	131 <option value="Pastel2_r">Pastel2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	132 <option value="spring_r">spring reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	133 <option value="summer_r">summer reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	134 <option value="autumn_r">autumn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	135 <option value="winter_r">winter reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	136 <option value="hot_r">hot reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	137 <option value="coolwarm_r">coolwarm reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	138 <option value="cool_r">cool reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	139 <option value="seismic_r">seismic reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	140 <option value="terrain_r">terrain reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	141 <option value="ocean_r">ocean reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	142 <option value="rainbow_r">rainbow reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	143 <option value="bone_r">bone reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	144 <option value="flag_r">flag reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	145 <option value="prism_r">prism reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	146 <option value="cubehelix_r">cubehelix reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	147 <option value="binary_r">binary reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	148 <option value="pink_r">pink reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	149 <option value="gray_r">gray reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	150 <option value="copper_r">copper reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	151 <option value="BrBG_r">BrBG reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	152 <option value="BuGn_r">BuGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	153 <option value="BuPu_r">BuPu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	154 <option value="GnBu_r">GnBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	155 <option value="OrRd_r">OrRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	156 <option value="PiYG_r">PiYG reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	157 <option value="PRGn_r">PRGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	158 <option value="PuOr_r">PuOr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	159 <option value="PuRd_r">PuRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	160 <option value="PuBu_r">PuBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	161 <option value="RdBu_r">RdBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	162 <option value="RdGy_r">RdGy reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	163 <option value="RdPu_r">RdPu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	164 <option value="YlGn_r">YlGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	165 <option value="PuBuGn_r">PuBuGn reversed</option>
1 a6ccec9faaa3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: 0 diff changeset	166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	167 <option value="RdYlGn_r">RdYlGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	168 <option value="YlGnBu_r">YlGnBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	169 <option value="YlOrBr_r">YlOrBr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	170 <option value="YlOrRd_r">YlOrRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	171 <option value="gist_gray_r">gist_gray reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	172 <option value="gist_stern_r">gist_stern reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	173 <option value="gist_earth_r">gist_earth reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	174 <option value="gist_yarg_r">gist_yarg reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	175 <option value="gist_ncar_r">gist_ncar reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	176 <option value="gist_rainbow_r">gist_rainbow reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	177 <option value="gist_heat_r">gist_heat reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	178 <option value="gnuplot_r">gnuplot reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	179 <option value="gnuplot2_r">gnuplot2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	180 <option value="CMRmap_r">CMRmap reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	181 <option value="bwr_r">bwr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	182 <option value="hsv_r">hsv reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	183 <option value="brg_r">brg reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	184 <option value="jet_r">jet reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	185 <option value="afmhot_r">afmhot reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	186 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	187 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	188
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	189
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	190 <xml name="multiple_input_matrices">
10 551510b684b7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	191 <repeat name="input_files" title="Hi-C Matrix files" min="2">
6 784c054ce4a1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	192 <param name="matrix" type="data" format="h5,cool"
10 551510b684b7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	193 label="Hi-C Matrix file"
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	194 help=""/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	195 <param name="mlabel" type="text" size="30" optional="true" value=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	196 label="Label"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	197 help="Label to use in the output. If not given the dataset name will be used instead."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	198 </repeat>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	199 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	200
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	201 <token name="@multiple_input_matrices@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	202 #set $matrices = []
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	203 #set $mlabels = []
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	204 #for $counter, $i in enumerate($input_files):
6 784c054ce4a1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	205 ln -s $i.matrix #echo str($counter)+'_matrix'#;
784c054ce4a1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	206 #silent $matrices.append( '%s_matrix' % $counter )
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	207
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	208 #if str($i.mlabel.value) != "":
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	210 #else
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	211 #set $mlabels += ['"%s"' % ($i.matrix.name)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	212 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	213 #end for
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	214 #set $mlabels = ' '.join($mlabels)
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	215 #set $matrices = ' '.join($matrices)
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	216 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	217
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	218
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	219 <xml name="region">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	220 <param name="region" type="text" label="Region of the genome to limit the operation"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	222 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	223
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	224
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	225
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	226 <xml name="kmeans_clustering">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	227 <conditional name="used_multiple_regions">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	228 <param name="used_multiple_regions_options" type="select"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	229 label="Did you compute the matrix with more than one groups of regions?"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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.">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	231 <option value="yes">Yes, I used multiple groups of regions</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	232 <option value="no">No, I used only one group</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	233 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	234 <when value="no">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	235 <conditional name="clustering">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	236 <param name="clustering_options" type="select" label="Clustering algorithm">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	237 <option value="none">No clustering</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	238 <option value="kmeans">Kmeans clustering</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	239 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	240 <when value="kmeans">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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)."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	243 </when>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	244 <when value="none" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	245 </conditional>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	246 </when>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	247 <when value="yes" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	248 </conditional>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	249 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	250
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	251 <token name="@KMEANS_CLUSTERING@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	256 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	257 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	258 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	259 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	260
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	261 <xml name="samFlag">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	262 <param name="samFlag" type="integer" optional="true" value=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	263 label="Filter reads based on the SAM flag"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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)"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	265 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	266 <xml name="plotNumbers">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	268 label="Plot the correlation value"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	270 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	271 <xml name="doNotExtendPairedEnds">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	273 label="Do not extend paired ends"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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)"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	275 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	276
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	277 <xml name="ignoreDuplicates">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	279 label="Ignore duplicates"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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)" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	281 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	282
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	283 <xml name="minMappingQuality">
1 a6ccec9faaa3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: 0 diff changeset	284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	285 label="Minimum mapping quality"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	286 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	287 Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	289 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	290
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	291 <xml name="skipZeros">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	293 label ="Skip zeros"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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)" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	295 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	296
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	297 <xml name="fragmentLength">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	298 <param name="fragmentLength" type="integer" value="300" min="1"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	299 label="Fragment length used for the sequencing"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	301 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	302
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	303 <xml name="scaleFactor">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	306 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	307
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	308 <xml name="xMax">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	309 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	310 label="Max value for the x-axis in counts per bin" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	311 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	312
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	313 <xml name="filterThreshold">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	316
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	319 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	320
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	321
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	322 <xml name="pseudocount">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	323 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	324 </xml>
6 784c054ce4a1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	325 <xml name='matrix_h5_cooler_macro'>
9 673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	326 <param name='matrix_h5_cooler' type="data" format="h5,cool"
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	327 label="Matrix to compute on"/>
6 784c054ce4a1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	328 </xml>
784c054ce4a1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	329 <xml name='matrix_h5_cooler_multiple_macro'>
9 673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	330 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	331 label="Matricies to compute on" multiple="true"/>
6 784c054ce4a1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	332 </xml>
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	333 <token name="@REFERENCES@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	334
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	335 .. class:: infomark
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	336
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	337 For more information on the tools, please visit our `help site`_.
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	338
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	340
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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`_.
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	342
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	343 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	344 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
3 81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	345 .. _help site: https://hicexplorer.readthedocs.org
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	346
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	347 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	348
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	349
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	350 <xml name="multiple_input_bams">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	351 <repeat name="input_files" title="BAM files" min="2">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	352 <param name="bamfile" type="data" format="bam"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	353 label="Bam file"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	354 help="The BAM file must be sorted."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	355 <param name="label" type="text" size="30" optional="true" value=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	356 label="Label"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	357 help="Label to use in the output. If not given the dataset name will be used instead."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	358 </repeat>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	359 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	360
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	361 <xml name="multiple_input_bigwigs">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	362 <repeat name="input_files" title="BigWig files" min="2">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	363 <param name="bigwigfile" type="data" format="bigwig"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	364 label="Bigwig file"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	365 help="The Bigwig file must be sorted."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	366 <param name="label" type="text" size="30" optional="true" value=""
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	367 label="Label"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	368 help="Label to use in the output. If not given the dataset name will be used instead."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	369 </repeat>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	370 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	371
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	372 <xml name="plotTitle">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	373 <param name="plotTitle" type="text" value="" size="30" optional="True"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	374 label="Title of the plot"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	375 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	376 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	377
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	378 <token name="@multiple_input_bams@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	379 #import tempfile
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	380 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	381 #set files=[]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	382 #set labels=[]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	383 #for $i in $input_files:
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	385 #set $temp_input_path = $temp_input_handle.name
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	386 #silent $temp_input_handle.close()
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	387 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	388 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	389 #silent $files.append('%s.bam' % $temp_input_path)
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	390
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	391 ##set $files += [str($i.bamfile)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	392 #if str($i.label.value) != "":
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	393 #set $labels += ["\"%s\"" % ($i.label.value)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	394 #else
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	395 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	396 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	397 #end for
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	398 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	399
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	400 <token name="@multiple_input_bigwigs@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	401 #import tempfile
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	402 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	403 #set files=[]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	404 #set labels=[]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	405 #for $i in $input_files:
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	406 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	407 #set $temp_input_path = $temp_input_handle.name
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	408 #silent $temp_input_handle.close()
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	409 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	410 #silent $files.append('%s.bw' % $temp_input_path)
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	411
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	412 ##set $files += [str($i.bigwigfile)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	413 #if str($i.label.value) != "":
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	414 #set $labels += ["\"%s\"" % ($i.label.value)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	415 #else
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	416 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	417 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	418 #end for
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	419 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	420
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	421 <xml name="reference_genome_source">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	422 <conditional name="source">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	423 <param name="ref_source" type="select" label="Reference genome">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	424 <option value="cached">locally cached</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	425 <option value="history">in your history</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	426 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	427 <when value="cached">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	429 <options from_data_table="deepTools_seqs">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	430 <filter type="sort_by" column="1" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	431 <validator type="no_options" message="No indexes are available." />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	432 </options>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	433 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	434 </when>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	435 <when value="history">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	436 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	437 </when>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	438 </conditional>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	439 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	440
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	441 <token name="@reference_genome_source@">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	442 #if $source.ref_source=="history":
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	443 --genome $source.input1
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	444 #else:
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	445 --genome "${source.input1_2bit.fields.path}"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	446 #end if
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	447 </token>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	448
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	449 <xml name="effectiveGenomeSize">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	450 <conditional name="effectiveGenomeSize">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	451 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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.
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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.
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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.">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	455 <option value="93260000">ce10 (93260000)</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	456 <option value="121400000">dm3 (121400000)</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	457 <option value="2451960000" selected="true">hg19 (2451960000)</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	458 <option value="2150570000">mm9 (2150570000)</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	459 <option value="specific">user specified</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	460 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	461 <when value="specific">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	463 </when>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	464 <when value="2150570000" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	465 <when value="2451960000" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	466 <when value="121400000" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	467 <when value="93260000" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	468 </conditional>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	469 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	470
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	471 <xml name="image_file_format">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	472 <param name="outFileFormat" type="select" label="Image file format">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	473 <option value="png" selected="true">png</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	474 <option value="pdf">pdf</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	475 <option value="svg">svg</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	476 <option value="eps">eps</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	477 <option value="emf">emf</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	478 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	479 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	480
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	481 <xml name="missingDataAsZero">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	482 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	483 label ="Treat missing data as zero"
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty 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." />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	485 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	486
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	487 <xml name="input_save_matrix_values">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	488 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	489 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	490
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	491 <xml name="input_graphic_output_settings">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	492 <conditional name="output" >
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	493 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	494 <option value="no" selected="true">no</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	495 <option value="yes">yes</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	496 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	497 <when value="no" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	498 <when value="yes">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	499 <yield />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	500 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	501 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	502 </when>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	503 </conditional>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	504 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	505
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	506 <xml name="input_image_file_format">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	507 <param name="outFileFormat" type="select" label="Image file format">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	508 <option value="png" selected="true">png</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	509 <option value="pdf">pdf</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	510 <option value="svg">svg</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	511 <option value="eps">eps</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	512 <option value="emf">emf</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	513 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	514 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	515
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	516 <xml name="output_image_file_format">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	517 <data format="png" name="outFileName" label="${tool.name} image">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	518 <change_format>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	519 <when input="output.outFileFormat" value="pdf" format="pdf" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	520 <when input="output.outFileFormat" value="svg" format="svg" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	521 <when input="output.outFileFormat" value="eps" format="eps" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	522 <when input="output.outFileFormat" value="emf" format="emf" />
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	523 </change_format>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	524 </data>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	525 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	526
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	527 <xml name="output_save_matrix_values">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	528 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	529 <filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	530 ((
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	531 output['showOutputSettings'] == 'yes' and
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	532 output['saveMatrix'] is True
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	533 ))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	534 </filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	535 </data>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	536 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	537
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	538 <xml name="output_graphic_outputs">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	539 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	540 <filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	541 ((
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	542 output['showOutputSettings'] == 'yes' and
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	543 output['saveData'] is True
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	544 ))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	545 </filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	546 </data>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	547 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	548 <filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	549 ((
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	550 output['showOutputSettings'] == 'yes' and
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	551 output['saveSortedRegions'] is True
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	552 ))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	553 </filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	554 </data>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	555 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	556
3 81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	557 <xml name="track_input_h5_macro">
6 784c054ce4a1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	558 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
3 81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	559 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	560 <xml name="track_input_bed_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	561 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	562 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	563 <xml name="track_input_bedgraph_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	564 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	565 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	566 <xml name="track_input_bigwig_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	567 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	568 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	569 <xml name="track_input_bedgraph_matrix_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	570 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	571 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	572 <xml name="track_input_tabular_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	573 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	574 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	575 <xml name="plot_title">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	576 <param name="title" type="text" optional="true" label="Plot title"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	577 </xml>
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	578
3 81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	579 <xml name="spacer_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	580 <param name="spacer_width" type="float" value="" optional="True"
9 673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	581 label="Include spacer at the end of the track." help="Width of the spacer." />
3 81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	582 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	583 <xml name="fontsize_macro">
9 673c3280e576 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	584 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
3 81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	585 </xml>
0 f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	586 </macros>

Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate macros.xml @ 10:551510b684b7 draft