hicexplorer_hicbuildmatrix: macros.xml annotate

annotate macros.xml @ 14:d5c7bf85dd93 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"

author	iuc
date	Mon, 09 Dec 2019 10:27:01 +0000
parents	706936009fb7
children	f90c9c383fb2

rev	line source
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	1 <macros>
3 41d4044e1dfe 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>
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	3 <token name="@WRAPPER_VERSION@">3.3.1</token>
9 079757596dee 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@">
079757596dee 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":
079757596dee 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
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	7 #end if
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	8 </token>
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	9
0 611b0f02e109 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">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	11 <requirements>
611b0f02e109 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>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	13 <yield />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	14 </requirements>
611b0f02e109 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>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	16 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	17
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	18 <token name="@CHROMOSOME_LIST@">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	19 #if $chromosome_list:
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	20 #set $chromosomes = []
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	21 #for $chrom in $chromosome_list:
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	22 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	23 #end for
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	24 #set $chromosome_string = ' '.join($chromosomes)
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	25 --chromosomes $chromosome_string
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	26 #end if
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	27 </token>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	28
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	29 <xml name="chromosome_list">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	30 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	31 <param argument="--chromosomes" type="text" value="" >
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	32 <validator type="empty_field" />
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	33 </param>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	34 </repeat>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	35 </xml>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	36
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	37 <xml name="citations">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	38 <citations>
7 7c5b8da3a052 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058 iuc parents: 6 diff changeset	39 <citation type="doi">10.5281/zenodo.1133705</citation>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	40 <yield />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	41 </citations>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	42 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	43
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	44 <xml name="zMax">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	45 <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 -->
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	46 </xml>
9 079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	47 <xml name="use_range">
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	48 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
10 ee5a82a286ed planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	49 <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 079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	50 <option value="no_use_range">No restriction</option>
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	51 <option value="yes_use_range">Only consider counts within a range</option>
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	52 </param>
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	53 <when value="no_use_range"/>
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	54 <when value="yes_use_range">
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	55 <expand macro='range' />
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	56 </when>
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	57 </conditional>
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	58 </xml>
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	59
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	60 <xml name="range">
10 ee5a82a286ed planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	61 <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."/>
ee5a82a286ed planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	62 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
9 079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	63 </xml>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	64
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	65 <xml name="colormap">
5 654282127b45 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04 iuc parents: 4 diff changeset	66 <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 8ffb4beeabcf planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: 0 diff changeset	67 <option value="RdYlBu">RdYlBu</option>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	68 <option value="Accent">Accent</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	69 <option value="Spectral">Spectral</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	70 <option value="Set1">Set1</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	71 <option value="Set2">Set2</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	72 <option value="Set3">Set3</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	73 <option value="Dark2">Dark2</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	74 <option value="Reds">Reds</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	75 <option value="Oranges">Oranges</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	76 <option value="Greens">Greens</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	77 <option value="Blues">Blues</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	78 <option value="Greys">Greys</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	79 <option value="Purples">Purples</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	80 <option value="Paired">Paired</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	81 <option value="Pastel1">Pastel1</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	82 <option value="Pastel2">Pastel2</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	83 <option value="spring">spring</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	84 <option value="summer">summer</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	85 <option value="autumn">autumn</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	86 <option value="winter">winter</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	87 <option value="hot">hot</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	88 <option value="coolwarm">coolwarm</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	89 <option value="cool">cool</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	90 <option value="seismic">seismic</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	91 <option value="terrain">terrain</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	92 <option value="ocean">ocean</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	93 <option value="rainbow">rainbow</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	94 <option value="bone">bone</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	95 <option value="flag">flag</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	96 <option value="prism">prism</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	97 <option value="cubehelix">cubehelix</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	98 <option value="binary">binary</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	99 <option value="pink">pink</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	100 <option value="gray">gray</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	101 <option value="copper">copper</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	102 <option value="BrBG">BrBG</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	103 <option value="BuGn">BuGn</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	104 <option value="BuPu">BuPu</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	105 <option value="GnBu">GnBu</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	106 <option value="OrRd">OrRd</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	107 <option value="PiYG">PiYG</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	108 <option value="PRGn">PRGn</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	109 <option value="PuOr">PuOr</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	110 <option value="PuRd">PuRd</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	111 <option value="PuBu">PuBu</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	112 <option value="RdBu">RdBu</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	113 <option value="RdGy">RdGy</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	114 <option value="RdPu">RdPu</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	115 <option value="YlGn">YlGn</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	116 <option value="PuBuGn">PuBuGn</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	117 <option value="RdYlGn">RdYlGn</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	118 <option value="YlGnBu">YlGnBu</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	119 <option value="YlOrBr">YlOrBr</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	120 <option value="YlOrRd">YlOrRd</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	121 <option value="gist_gray">gist_gray</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	122 <option value="gist_stern">gist_stern</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	123 <option value="gist_earth">gist_earth</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	124 <option value="gist_yarg">gist_yarg</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	125 <option value="gist_ncar">gist_ncar</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	126 <option value="gist_rainbow">gist_rainbow</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	127 <option value="gist_heat">gist_heat</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	128 <option value="gnuplot">gnuplot</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	129 <option value="gnuplot2">gnuplot2</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	130 <option value="CMRmap">CMRmap</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	131 <option value="bwr">bwr</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	132 <option value="hsv">hsv</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	133 <option value="brg">brg</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	134 <option value="jet">jet</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	135 <option value="afmhot">afmhot</option>
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	136 <option value="plasma">plasma</option>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	137 <option value="Accent_r">Accent reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	138 <option value="Spectral_r">Spectral reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	139 <option value="Set1_r">Set1 reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	140 <option value="Set2_r">Set2 reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	141 <option value="Set3_r">Set3 reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	142 <option value="Dark2_r">Dark2 reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	143 <option value="Reds_r">Reds reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	144 <option value="Oranges_r">Oranges reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	145 <option value="Greens_r">Greens reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	146 <option value="Blues_r">Blues reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	147 <option value="Greys_r">Greys reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	148 <option value="Purples_r">Purples reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	149 <option value="Paired_r">Paired reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	150 <option value="Pastel1_r">Pastel1 reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	151 <option value="Pastel2_r">Pastel2 reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	152 <option value="spring_r">spring reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	153 <option value="summer_r">summer reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	154 <option value="autumn_r">autumn reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	155 <option value="winter_r">winter reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	156 <option value="hot_r">hot reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	157 <option value="coolwarm_r">coolwarm reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	158 <option value="cool_r">cool reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	159 <option value="seismic_r">seismic reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	160 <option value="terrain_r">terrain reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	161 <option value="ocean_r">ocean reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	162 <option value="rainbow_r">rainbow reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	163 <option value="bone_r">bone reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	164 <option value="flag_r">flag reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	165 <option value="prism_r">prism reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	166 <option value="cubehelix_r">cubehelix reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	167 <option value="binary_r">binary reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	168 <option value="pink_r">pink reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	169 <option value="gray_r">gray reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	170 <option value="copper_r">copper reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	171 <option value="BrBG_r">BrBG reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	172 <option value="BuGn_r">BuGn reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	173 <option value="BuPu_r">BuPu reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	174 <option value="GnBu_r">GnBu reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	175 <option value="OrRd_r">OrRd reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	176 <option value="PiYG_r">PiYG reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	177 <option value="PRGn_r">PRGn reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	178 <option value="PuOr_r">PuOr reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	179 <option value="PuRd_r">PuRd reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	180 <option value="PuBu_r">PuBu reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	181 <option value="RdBu_r">RdBu reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	182 <option value="RdGy_r">RdGy reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	183 <option value="RdPu_r">RdPu reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	184 <option value="YlGn_r">YlGn reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	185 <option value="PuBuGn_r">PuBuGn reversed</option>
1 8ffb4beeabcf planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: 0 diff changeset	186 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	187 <option value="RdYlGn_r">RdYlGn reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	188 <option value="YlGnBu_r">YlGnBu reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	189 <option value="YlOrBr_r">YlOrBr reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	190 <option value="YlOrRd_r">YlOrRd reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	191 <option value="gist_gray_r">gist_gray reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	192 <option value="gist_stern_r">gist_stern reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	193 <option value="gist_earth_r">gist_earth reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	194 <option value="gist_yarg_r">gist_yarg reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	195 <option value="gist_ncar_r">gist_ncar reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	196 <option value="gist_rainbow_r">gist_rainbow reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	197 <option value="gist_heat_r">gist_heat reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	198 <option value="gnuplot_r">gnuplot reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	199 <option value="gnuplot2_r">gnuplot2 reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	200 <option value="CMRmap_r">CMRmap reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	201 <option value="bwr_r">bwr reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	202 <option value="hsv_r">hsv reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	203 <option value="brg_r">brg reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	204 <option value="jet_r">jet reversed</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	205 <option value="afmhot_r">afmhot reversed</option>
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	206 <option value="plasma_r">plasma reversed</option>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	207 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	208 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	209
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	210 <xml name="multiple_input_matrices">
10 ee5a82a286ed planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	211 <repeat name="input_files" title="Hi-C Matrix files" min="2">
6 747a789ce63c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	212 <param name="matrix" type="data" format="h5,cool"
10 ee5a82a286ed planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 9 diff changeset	213 label="Hi-C Matrix file"
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	214 help=""/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	215 <param name="mlabel" type="text" size="30" optional="true" value=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	216 label="Label"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	217 help="Label to use in the output. If not given the dataset name will be used instead."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	218 </repeat>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	219 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	220
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	221 <token name="@multiple_input_matrices@">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	222 #set $matrices = []
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	223 #set $mlabels = []
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	224 #for $counter, $i in enumerate($input_files):
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	225 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	226 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	227
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	228 #if str($i.mlabel.value) != "":
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	229 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	230 #else
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	231 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	232 #end if
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	233 #end for
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	234 #set $mlabels = ' '.join($mlabels)
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	235 #set $matrices = ' '.join($matrices)
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	236 </token>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	237
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	238 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	239 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	240 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	241
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	242 <xml name="region">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	243 <param name="region" type="text" label="Region of the genome to limit the operation"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	244 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	245 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	246
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	247
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	248
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	249 <xml name="kmeans_clustering">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	250 <conditional name="used_multiple_regions">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	251 <param name="used_multiple_regions_options" type="select"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	252 label="Did you compute the matrix with more than one groups of regions?"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	253 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.">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	254 <option value="yes">Yes, I used multiple groups of regions</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	255 <option value="no">No, I used only one group</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	256 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	257 <when value="no">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	258 <conditional name="clustering">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	259 <param name="clustering_options" type="select" label="Clustering algorithm">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	260 <option value="none">No clustering</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	261 <option value="kmeans">Kmeans clustering</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	262 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	263 <when value="kmeans">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	264 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	265 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)."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	266 </when>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	267 <when value="none" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	268 </conditional>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	269 </when>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	270 <when value="yes" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	271 </conditional>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	272 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	273
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	274 <token name="@KMEANS_CLUSTERING@">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	275 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	276 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	277 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	278 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	279 #end if
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	280 #end if
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	281 #end if
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	282 </token>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	283
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	284 <xml name="samFlag">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	285 <param name="samFlag" type="integer" optional="true" value=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	286 label="Filter reads based on the SAM flag"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	287 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)"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	288 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	289 <xml name="plotNumbers">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	290 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	291 label="Plot the correlation value"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	292 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	293 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	294 <xml name="doNotExtendPairedEnds">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	295 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	296 label="Do not extend paired ends"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	297 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)"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	298 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	299
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	300 <xml name="ignoreDuplicates">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	301 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	302 label="Ignore duplicates"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	303 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)" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	304 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	305
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	306 <xml name="minMappingQuality">
1 8ffb4beeabcf planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: 0 diff changeset	307 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	308 label="Minimum mapping quality"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	309 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	310 Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	311 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."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	312 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	313
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	314 <xml name="skipZeros">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	315 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	316 label ="Skip zeros"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	317 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)" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	318 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	319
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	320 <xml name="fragmentLength">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	321 <param name="fragmentLength" type="integer" value="300" min="1"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	322 label="Fragment length used for the sequencing"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	323 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	324 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	325
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	326 <xml name="scaleFactor">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	327 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	328 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	329 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	330
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	331 <xml name="xMax">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	332 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	333 label="Max value for the x-axis in counts per bin" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	334 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	335
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	336 <xml name="filterThreshold">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	337 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	338 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	339
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	340 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	341 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	342 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	343
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	344
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	345 <xml name="pseudocount">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	346 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	347 </xml>
6 747a789ce63c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	348 <xml name='matrix_h5_cooler_macro'>
9 079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	349 <param name='matrix_h5_cooler' type="data" format="h5,cool"
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	350 label="Matrix to compute on"/>
6 747a789ce63c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	351 </xml>
747a789ce63c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	352 <xml name='matrix_h5_cooler_multiple_macro'>
9 079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	354 label="Matricies to compute on" multiple="true"/>
6 747a789ce63c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	355 </xml>
14 d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	356
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	357
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	358
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	359 <xml name='convertFormat_single_macro'>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	360 <conditional name="inputFormat_conditional">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	361 <param name="inputFormat_selector" type="select" label="Choose input file type">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	362 <option value="optionCool" selected="True">cool</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	363 <option value="optionH5">h5</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	364 <!-- <option value="optionHic">hic</option> -->
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	365 <option value="optionHomer">Homer</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	366 <option value="optionHicpro">HiCPro</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	367 </param>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	368 <when value="optionCool">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	369 <expand macro='matrix_h5_cooler_macro' />
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	370 <param name='correctionName' type='text' label='Correction factors column name'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	372 <param name='chromosome' type='text' label='Load only one chromosome'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	374
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	375 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	376 <when value="optionH5">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	377 <expand macro='matrix_h5_cooler_macro' />
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	378 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	379 <!-- <when value="optionHic">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	380 <param name='matrixHic' type='data' format='binary' label='.hic matrix'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	381 <param name='resolutions' type='text' label='List of resolutions'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	382 </when> -->
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	383
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	384 <when value="optionHomer">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	386 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	387
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	388 <when value="optionHicpro">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	389 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	390 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	391 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	392 </conditional>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	393 </xml>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	394
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	395 <xml name='convertFormat_multiple_macro'>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	396 <conditional name="inputFormat_conditional">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	397 <param name="inputFormat_selector" type="select" label="Choose input file type">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	398 <option value="optionCool" selected="True">cool</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	399 <option value="optionH5">h5</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	400 <option value="optionHomer">Homer</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	401 <option value="optionHicpro">HiCPro</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	402 </param>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	403 <when value="optionCool">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	404 <expand macro='matrix_h5_cooler_multiple_macro' />
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	405 <param name='correctionName' type='text' label='Correction factors column name'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	406 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	407 <param name='chromosome' type='text' label='Load only one chromosome'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	408 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	409
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	410 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	411 <when value="optionH5">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	412 <expand macro='matrix_h5_cooler_multiple_macro' />
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	413 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	414
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	415 <when value="optionHomer">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	416 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	417 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	418
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	419 <when value="optionHicpro">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	420 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	421 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	422 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	423 </conditional>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	424 </xml>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	425 <xml name='convertFormat_single_output_macro'>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	426 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	427
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	428 <conditional name="outputFormat_conditional">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	429 <param name="outputFormat_selector" type="select" label="Choose output file type">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	430 <option value="cool" selected="True">cool</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	431 <option value="h5">h5</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	432 <option value="homer">Homer</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	433 <option value="ginteractions">ginteractions</option>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	434
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	435 </param>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	436 <when value="cool">
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	437 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	438 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	439 </when>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	440 <when value='h5'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	441 <when value='homer'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	442 <when value='ginteractions'/>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	443
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	444 </conditional>
d5c7bf85dd93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391" iuc parents: 13 diff changeset	445 </xml>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	446 <token name="@REFERENCES@">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	447
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	448 .. class:: infomark
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	449
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	450 For more information on the tools, please visit our `help site`_.
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	451
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	452 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	453
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	454 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	455
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	456 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
3 41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	458 .. _help site: https://hicexplorer.readthedocs.org
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	459
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	460 </token>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	461
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	462
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	463 <xml name="multiple_input_bams">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	464 <repeat name="input_files" title="BAM files" min="2">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	465 <param name="bamfile" type="data" format="bam"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	466 label="Bam file"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	467 help="The BAM file must be sorted."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	468 <param name="label" type="text" size="30" optional="true" value=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	469 label="Label"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	470 help="Label to use in the output. If not given the dataset name will be used instead."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	471 </repeat>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	472 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	473
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	474 <xml name="multiple_input_bigwigs">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	475 <repeat name="input_files" title="BigWig files" min="2">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	476 <param name="bigwigfile" type="data" format="bigwig"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	477 label="Bigwig file"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	478 help="The Bigwig file must be sorted."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	479 <param name="label" type="text" size="30" optional="true" value=""
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	480 label="Label"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	481 help="Label to use in the output. If not given the dataset name will be used instead."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	482 </repeat>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	483 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	484
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	485 <xml name="plotTitle">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	486 <param name="plotTitle" type="text" value="" size="30" optional="True"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	487 label="Title of the plot"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	489 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	490
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	491 <token name="@multiple_input_bams@">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	492 #import tempfile
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	494 #set files=[]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	495 #set labels=[]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	496 #for $i in $input_files:
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	497 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	498 #set $temp_input_path = $temp_input_handle.name
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	499 #silent $temp_input_handle.close()
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	500 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	501 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	502 #silent $files.append('%s.bam' % $temp_input_path)
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	503
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	504 ##set $files += [str($i.bamfile)]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	505 #if str($i.label.value) != "":
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	506 #set $labels += ["\"%s\"" % ($i.label.value)]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	507 #else
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	508 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	509 #end if
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	510 #end for
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	511 </token>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	512
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	513 <token name="@multiple_input_bigwigs@">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	514 #import tempfile
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	515 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	516 #set files=[]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	517 #set labels=[]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	518 #for $i in $input_files:
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	519 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	520 #set $temp_input_path = $temp_input_handle.name
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	521 #silent $temp_input_handle.close()
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	522 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	523 #silent $files.append('%s.bw' % $temp_input_path)
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	524
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	525 ##set $files += [str($i.bigwigfile)]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	526 #if str($i.label.value) != "":
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	527 #set $labels += ["\"%s\"" % ($i.label.value)]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	528 #else
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	529 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	530 #end if
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	531 #end for
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	532 </token>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	533
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	534 <xml name="reference_genome_source">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	535 <conditional name="source">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	536 <param name="ref_source" type="select" label="Reference genome">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	537 <option value="cached">locally cached</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	538 <option value="history">in your history</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	539 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	540 <when value="cached">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	541 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	542 <options from_data_table="deepTools_seqs">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	543 <filter type="sort_by" column="1" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	544 <validator type="no_options" message="No indexes are available." />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	545 </options>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	546 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	547 </when>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	548 <when value="history">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	549 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	550 </when>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	551 </conditional>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	552 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	553
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	554 <token name="@reference_genome_source@">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	555 #if $source.ref_source=="history":
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	556 --genome $source.input1
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	557 #else:
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	558 --genome "${source.input1_2bit.fields.path}"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	559 #end if
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	560 </token>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	561
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	562 <xml name="effectiveGenomeSize">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	563 <conditional name="effectiveGenomeSize">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	564 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	565 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.
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	566 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	567 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.">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	568 <option value="93260000">ce10 (93260000)</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	569 <option value="121400000">dm3 (121400000)</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	570 <option value="2451960000" selected="true">hg19 (2451960000)</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	571 <option value="2150570000">mm9 (2150570000)</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	572 <option value="specific">user specified</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	573 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	574 <when value="specific">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	575 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	576 </when>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	577 <when value="2150570000" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	578 <when value="2451960000" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	579 <when value="121400000" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	580 <when value="93260000" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	581 </conditional>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	582 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	583
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	584 <xml name="image_file_format">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	585 <param name="outFileFormat" type="select" label="Image file format">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	586 <option value="png" selected="true">png</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	587 <option value="pdf">pdf</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	588 <option value="svg">svg</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	589 <option value="eps">eps</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	590 <option value="emf">emf</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	591 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	592 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	593
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	594 <xml name="missingDataAsZero">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	595 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	596 label ="Treat missing data as zero"
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	597 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." />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	598 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	599
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	600 <xml name="input_save_matrix_values">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	601 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	602 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	603
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	604 <xml name="input_graphic_output_settings">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	605 <conditional name="output" >
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	606 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	607 <option value="no" selected="true">no</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	608 <option value="yes">yes</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	609 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	610 <when value="no" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	611 <when value="yes">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	612 <yield />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	613 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	614 <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."/>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	615 </when>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	616 </conditional>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	617 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	618
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	619 <xml name="input_image_file_format">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	620 <param name="outFileFormat" type="select" label="Image file format">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	621 <option value="png" selected="true">png</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	622 <option value="pdf">pdf</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	623 <option value="svg">svg</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	624 <option value="eps">eps</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	625 <option value="emf">emf</option>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	626 </param>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	627 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	628
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	629 <xml name="output_image_file_format">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	630 <data format="png" name="outFileName" label="${tool.name} image">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	631 <change_format>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	632 <when input="output.outFileFormat" value="pdf" format="pdf" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	633 <when input="output.outFileFormat" value="svg" format="svg" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	634 <when input="output.outFileFormat" value="eps" format="eps" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	635 <when input="output.outFileFormat" value="emf" format="emf" />
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	636 </change_format>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	637 </data>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	638 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	639
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	640 <xml name="output_save_matrix_values">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	641 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	642 <filter>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	643 ((
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	644 output['showOutputSettings'] == 'yes' and
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	645 output['saveMatrix'] is True
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	646 ))
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	647 </filter>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	648 </data>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	649 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	650
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	651 <xml name="output_graphic_outputs">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	652 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	653 <filter>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	654 ((
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	655 output['showOutputSettings'] == 'yes' and
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	656 output['saveData'] is True
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	657 ))
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	658 </filter>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	659 </data>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	660 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	661 <filter>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	662 ((
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	663 output['showOutputSettings'] == 'yes' and
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	664 output['saveSortedRegions'] is True
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	665 ))
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	666 </filter>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	667 </data>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	668 </xml>
611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	669
3 41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	670 <xml name="track_input_h5_macro">
6 747a789ce63c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 iuc parents: 5 diff changeset	671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
3 41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	672 </xml>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	673 <xml name="track_input_bed_macro">
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	675 </xml>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	676 <xml name="track_input_bedgraph_macro">
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	678 </xml>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	679 <xml name="track_input_bigwig_macro">
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	680 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	681 </xml>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	682 <xml name="track_input_bedgraph_matrix_macro">
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	684 </xml>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	685 <xml name="track_input_tabular_macro">
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	686 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	687 </xml>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	688 <xml name="plot_title">
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	689 <param name="title" type="text" optional="true" label="Plot title"/>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	690 </xml>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	691
3 41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	692 <xml name="spacer_macro">
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	693 <param name="spacer_width" type="float" value="" optional="True"
9 079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	694 label="Include spacer at the end of the track." help="Width of the spacer." />
3 41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	695 </xml>
41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	696 <xml name="fontsize_macro">
9 079757596dee planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d iuc parents: 7 diff changeset	697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
3 41d4044e1dfe planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 iuc parents: 2 diff changeset	698 </xml>
0 611b0f02e109 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty bgruening parents: diff changeset	699 </macros>

Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

annotate macros.xml @ 14:d5c7bf85dd93 draft