hicexplorer_hiccorrectmatrix: macros.xml annotate

annotate macros.xml @ 21:ea19190ce5e0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

author	iuc
date	Wed, 18 Oct 2023 10:20:07 +0000
parents	f5a37c3906cc
children	62b720dceb56

rev	line source
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	1 <macros>
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	3 <token name="@TOOL_VERSION@">3.7.2</token>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	4 <token name="@VERSION_SUFFIX@">0</token>
8 f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	5 <token name="@USE_RANGE@">
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	6 #if $use_range.select_use_range == "yes_use_range":
18 5443b2b1165f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c" iuc parents: 16 diff changeset	7 --range $use_range.range_min:$use_range.range_max
8 f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	8 #end if
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	9 </token>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	10
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	11 <xml name="requirements">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	12 <requirements>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	13 <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	14 <yield />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	15 </requirements>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	16 <version_command>@BINARY@ --version</version_command>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	17 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	18
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	19 <token name="@CHROMOSOME_LIST@">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	20 #if $chromosome_list:
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	21 #set $chromosomes = []
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	22 #for $chrom in $chromosome_list:
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	23 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	24 #end for
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	25 #set $chromosome_string = ' '.join($chromosomes)
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	26 --chromosomes $chromosome_string
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	27 #end if
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	28 </token>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	29
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	30 <xml name="chromosome_list">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	31 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	32 <param argument="--chromosomes" type="text" value="">
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	33 <validator type="empty_field" />
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	34 </param>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	35 </repeat>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	36 </xml>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	37
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	38 <xml name="citations">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	39 <citations>
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	40 <citation type="doi">10.1093/nar/gkaa220</citation>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	41 <citation type="doi">10.1093/nar/gky504</citation>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	42 <yield />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	43 </citations>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	44 </xml>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	45 <xml name="dpi">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	46 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	47 </xml>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	48
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	49 <xml name="restrictionCutFile">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	50 <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	51 (i.e. the region between one restriction site and the next)." />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	52 </xml>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	53
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	54 <xml name="restrictionSequence">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	55 <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	56 "dangling-ends". If not given, such statistics will not be available.">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	57 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	58 </param>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	59 </xml>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	60 <xml name="danglingSequence">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	61 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	62 Each restriction enzyme recognizes a different DNA sequence and,
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	63 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	64 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	65 For DpnII, the restriction site and dangling end sequence are the same: GATC.
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	66 This information is easily found on the description of the restriction enzyme.
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	67 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	68 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	69 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	70 </param>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	71 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	72
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	73 <xml name="zMax">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	74 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	75 <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	76 </xml>
8 f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	77 <xml name="use_range">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	78 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	79 <param name="select_use_range" argument="--range" type="select" label="Range restriction (in bp)" help="If given, only counts within the specified range are considered.">
8 f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	80 <option value="no_use_range">No restriction</option>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	81 <option value="yes_use_range">Only consider counts within a range</option>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	82 </param>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	83 <when value="no_use_range" />
8 f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	84 <when value="yes_use_range">
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	85 <expand macro='range' />
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	86 </when>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	87 </conditional>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	88 </xml>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	89
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	90 <xml name="range">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	91 <param name='range_min' type="integer" value="" min="0" label="Minimum range to consider interactions" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions." />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	92 <param name='range_max' type="integer" value="" min="0" label="Maximum range to consider interactions" />
8 f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	93 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	94
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	95 <xml name="colormap">
4 b55d7936cbe0 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04 iuc parents: 3 diff changeset	96 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	97 <option value="RdYlBu">RdYlBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	98 <option value="Accent">Accent</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	99 <option value="Spectral">Spectral</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	100 <option value="Set1">Set1</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	101 <option value="Set2">Set2</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	102 <option value="Set3">Set3</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	103 <option value="Dark2">Dark2</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	104 <option value="Reds">Reds</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	105 <option value="Oranges">Oranges</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	106 <option value="Greens">Greens</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	107 <option value="Blues">Blues</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	108 <option value="Greys">Greys</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	109 <option value="Purples">Purples</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	110 <option value="Paired">Paired</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	111 <option value="Pastel1">Pastel1</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	112 <option value="Pastel2">Pastel2</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	113 <option value="spring">spring</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	114 <option value="summer">summer</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	115 <option value="autumn">autumn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	116 <option value="winter">winter</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	117 <option value="hot">hot</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	118 <option value="coolwarm">coolwarm</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	119 <option value="cool">cool</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	120 <option value="seismic">seismic</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	121 <option value="terrain">terrain</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	122 <option value="ocean">ocean</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	123 <option value="rainbow">rainbow</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	124 <option value="bone">bone</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	125 <option value="flag">flag</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	126 <option value="prism">prism</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	127 <option value="cubehelix">cubehelix</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	128 <option value="binary">binary</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	129 <option value="pink">pink</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	130 <option value="gray">gray</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	131 <option value="copper">copper</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	132 <option value="BrBG">BrBG</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	133 <option value="BuGn">BuGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	134 <option value="BuPu">BuPu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	135 <option value="GnBu">GnBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	136 <option value="OrRd">OrRd</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	137 <option value="PiYG">PiYG</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	138 <option value="PRGn">PRGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	139 <option value="PuOr">PuOr</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	140 <option value="PuRd">PuRd</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	141 <option value="PuBu">PuBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	142 <option value="RdBu">RdBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	143 <option value="RdGy">RdGy</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	144 <option value="RdPu">RdPu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	145 <option value="YlGn">YlGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	146 <option value="PuBuGn">PuBuGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	147 <option value="RdYlGn">RdYlGn</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	148 <option value="YlGnBu">YlGnBu</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	149 <option value="YlOrBr">YlOrBr</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	150 <option value="YlOrRd">YlOrRd</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	151 <option value="gist_gray">gist_gray</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	152 <option value="gist_stern">gist_stern</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	153 <option value="gist_earth">gist_earth</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	154 <option value="gist_yarg">gist_yarg</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	155 <option value="gist_ncar">gist_ncar</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	156 <option value="gist_rainbow">gist_rainbow</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	157 <option value="gist_heat">gist_heat</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	158 <option value="gnuplot">gnuplot</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	159 <option value="gnuplot2">gnuplot2</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	160 <option value="CMRmap">CMRmap</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	161 <option value="bwr">bwr</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	162 <option value="hsv">hsv</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	163 <option value="brg">brg</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	164 <option value="jet">jet</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	165 <option value="afmhot">afmhot</option>
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	166 <option value="plasma">plasma</option>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	167 <option value="Accent_r">Accent reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	168 <option value="Spectral_r">Spectral reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	169 <option value="Set1_r">Set1 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	170 <option value="Set2_r">Set2 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	171 <option value="Set3_r">Set3 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	172 <option value="Dark2_r">Dark2 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	173 <option value="Reds_r">Reds reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	174 <option value="Oranges_r">Oranges reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	175 <option value="Greens_r">Greens reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	176 <option value="Blues_r">Blues reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	177 <option value="Greys_r">Greys reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	178 <option value="Purples_r">Purples reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	179 <option value="Paired_r">Paired reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	180 <option value="Pastel1_r">Pastel1 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	181 <option value="Pastel2_r">Pastel2 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	182 <option value="spring_r">spring reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	183 <option value="summer_r">summer reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	184 <option value="autumn_r">autumn reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	185 <option value="winter_r">winter reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	186 <option value="hot_r">hot reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	187 <option value="coolwarm_r">coolwarm reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	188 <option value="cool_r">cool reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	189 <option value="seismic_r">seismic reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	190 <option value="terrain_r">terrain reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	191 <option value="ocean_r">ocean reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	192 <option value="rainbow_r">rainbow reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	193 <option value="bone_r">bone reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	194 <option value="flag_r">flag reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	195 <option value="prism_r">prism reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	196 <option value="cubehelix_r">cubehelix reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	197 <option value="binary_r">binary reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	198 <option value="pink_r">pink reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	199 <option value="gray_r">gray reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	200 <option value="copper_r">copper reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	201 <option value="BrBG_r">BrBG reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	202 <option value="BuGn_r">BuGn reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	203 <option value="BuPu_r">BuPu reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	204 <option value="GnBu_r">GnBu reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	205 <option value="OrRd_r">OrRd reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	206 <option value="PiYG_r">PiYG reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	207 <option value="PRGn_r">PRGn reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	208 <option value="PuOr_r">PuOr reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	209 <option value="PuRd_r">PuRd reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	210 <option value="PuBu_r">PuBu reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	211 <option value="RdBu_r">RdBu reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	212 <option value="RdGy_r">RdGy reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	213 <option value="RdPu_r">RdPu reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	214 <option value="YlGn_r">YlGn reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	215 <option value="PuBuGn_r">PuBuGn reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	216 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	217 <option value="RdYlGn_r">RdYlGn reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	218 <option value="YlGnBu_r">YlGnBu reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	219 <option value="YlOrBr_r">YlOrBr reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	220 <option value="YlOrRd_r">YlOrRd reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	221 <option value="gist_gray_r">gist_gray reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	222 <option value="gist_stern_r">gist_stern reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	223 <option value="gist_earth_r">gist_earth reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	224 <option value="gist_yarg_r">gist_yarg reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	225 <option value="gist_ncar_r">gist_ncar reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	226 <option value="gist_rainbow_r">gist_rainbow reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	227 <option value="gist_heat_r">gist_heat reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	228 <option value="gnuplot_r">gnuplot reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	229 <option value="gnuplot2_r">gnuplot2 reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	230 <option value="CMRmap_r">CMRmap reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	231 <option value="bwr_r">bwr reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	232 <option value="hsv_r">hsv reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	233 <option value="brg_r">brg reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	234 <option value="jet_r">jet reversed</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	235 <option value="afmhot_r">afmhot reversed</option>
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	236 <option value="plasma_r">plasma reversed</option>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	237 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	238 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	239
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	240 <xml name="multiple_input_matrices">
9 ac80bd0a96ca planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 iuc parents: 8 diff changeset	241 <repeat name="input_files" title="Hi-C Matrix files" min="2">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	242 <param name="matrix" type="data" format="h5,cool" label="Hi-C Matrix file" help="" />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	243 <param name="mlabel" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	244 </repeat>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	245 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	246
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	247 <token name="@multiple_input_matrices@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	248 #set $matrices = []
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	249 #set $mlabels = []
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	250 #for $counter, $i in enumerate($input_files):
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	251 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	252 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	253
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	254 #if str($i.mlabel.value) != "":
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	255 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	256 #else
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	257 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	258 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	259 #end for
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	260 #set $mlabels = ' '.join($mlabels)
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	261 #set $matrices = ' '.join($matrices)
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	262 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	263
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	264 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	265 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	266 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	267
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	268 <xml name="region">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	269 <param argument="--region" type="text" label="Region of the genome to limit the operation" help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	270 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	271 </param>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	272 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	273
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	274 <xml name="kmeans_clustering">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	275 <conditional name="used_multiple_regions">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	276 <param name="used_multiple_regions_options" type="select" label="Did you compute the matrix with more than one groups of regions?" 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.">
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	277 <option value="yes">Yes, I used multiple groups of regions</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	278 <option value="no">No, I used only one group</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	279 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	280 <when value="no">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	281 <conditional name="clustering">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	282 <param name="clustering_options" type="select" label="Clustering algorithm">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	283 <option value="none">No clustering</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	284 <option value="kmeans">Kmeans clustering</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	285 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	286 <when value="kmeans">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	287 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 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)." />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	288 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	289 <when value="none" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	290 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	291 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	292 <when value="yes" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	293 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	294 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	295
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	296 <token name="@KMEANS_CLUSTERING@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	297 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	298 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	299 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	300 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	301 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	302 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	303 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	304 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	305
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	306 <xml name="samFlag">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	307 <param name="samFlag" type="integer" optional="true" value="" label="Filter reads based on the SAM flag" 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)" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	308 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	309 <xml name="plotNumbers">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	310 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" label="Plot the correlation value" help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	311 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	312 <xml name="doNotExtendPairedEnds">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	313 <param argument="--doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" label="Do not extend paired ends" 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)" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	314 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	315 <xml name="ignoreDuplicates">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	316 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" label="Ignore duplicates" 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)" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	317 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	318 <xml name="minMappingQuality">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	319 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" label="Minimum mapping quality" help= "If set, only reads that have a mapping quality score higher than the given value are considered.
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	320 Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	321 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." />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	322 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	323
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	324 <xml name="skipZeros">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	325 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label="Skip zeros" 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)" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	326 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	327
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	328 <xml name="fragmentLength">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	329 <param argument="--fragmentLength" type="integer" value="300" min="1" label="Fragment length used for the sequencing" help="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	330 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	331
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	332 <xml name="scaleFactor">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	333 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)" />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	334 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	335 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	336 <xml name="xMax">
20 f5a37c3906cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02 iuc parents: 19 diff changeset	337 <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	338 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	339 <xml name="filterThreshold">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	340 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	341 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect." />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	342 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	343 <xml name="pseudocount">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	344 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero." />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	345 </xml>
5 44919af9194b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 bgruening parents: 4 diff changeset	346 <xml name='matrix_h5_cooler_macro'>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	347 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" />
5 44919af9194b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 bgruening parents: 4 diff changeset	348 </xml>
44919af9194b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 bgruening parents: 4 diff changeset	349 <xml name='matrix_h5_cooler_multiple_macro'>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	350 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
5 44919af9194b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 bgruening parents: 4 diff changeset	351 </xml>
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	352
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	353 <xml name='matrix_cooler_multiple_macro'>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	354 <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	355 </xml>
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	356 <xml name='convertFormat_single_macro'>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	357 <conditional name="inputFormat_conditional">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	358 <param name="inputFormat_selector" type="select" label="Choose input file type">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	359 <option value="optionCool" selected="True">cool</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	360 <option value="optionH5">h5</option>
14 1e622e371512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064" bgruening parents: 13 diff changeset	361 <option value="optionHic">hic</option>
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	362 <option value="optionHomer">Homer</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	363 <option value="optionHicpro">HiCPro</option>
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	364 <option value="option2Dtext">2D-text</option>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	365
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	366 </param>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	367 <when value="optionCool">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	368 <expand macro='matrix_h5_cooler_macro' />
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	369 <param name='correctionName' type='text' label='Correction factors column name' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	370 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	371 <param name='chromosome' type='text' label='Load only one chromosome' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	372 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	373 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	374 <when value="optionH5">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	375 <expand macro='matrix_h5_cooler_macro' />
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	376 </when>
14 1e622e371512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064" bgruening parents: 13 diff changeset	377 <when value="optionHic">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	378 <param name='matrixHic' type='data' format='hic' label='.hic matrix' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	379 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	380 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	381 </param>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	382 </when>
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	383 <when value="optionHomer">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	384 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	385 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	386 <when value="optionHicpro">
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	387 <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	388 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	389 </when>
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	390 <when value="option2Dtext">
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	391 <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	392
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	393 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	394 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	395 </param>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	396 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	397 </when>
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	398 </conditional>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	399 </xml>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	400
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	401 <xml name='convertFormat_multiple_macro'>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	402 <conditional name="inputFormat_conditional">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	403 <param name="inputFormat_selector" type="select" label="Choose input file type">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	404 <option value="optionCool" selected="True">cool</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	405 <option value="optionH5">h5</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	406 <option value="optionHomer">Homer</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	407 <option value="optionHicpro">HiCPro</option>
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	408 <option value="option2Dtext">2D-text</option>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	409
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	410
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	411 </param>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	412 <when value="optionCool">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	413 <expand macro='matrix_h5_cooler_multiple_macro' />
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	414 <param name='correctionName' type='text' label='Correction factors column name' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	415 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	416 <param name='chromosome' type='text' label='Load only one chromosome' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	417 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	418 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	419 <when value="optionH5">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	420 <expand macro='matrix_h5_cooler_multiple_macro' />
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	421 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	422 <when value="optionHomer">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	423 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	424 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	425 <when value="optionHicpro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	426 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	427 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	428 </when>
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	429 <when value="option2Dtext">
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	430 <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	431
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	432 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	433 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	434 </param>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	435 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	436 </when>
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	437 </conditional>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	438 </xml>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	439 <xml name='convertFormat_single_output_macro'>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	440 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	441 <conditional name="outputFormat_conditional">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	442 <param name="outputFormat_selector" type="select" label="Choose output file type">
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	443 <option value="cool" selected="True">cool</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	444 <option value="h5">h5</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	445 <option value="homer">Homer</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	446 <option value="ginteractions">ginteractions</option>
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	447 <option value="hicpro">hicpro</option>
ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	448
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	449 </param>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	450 <when value="cool">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	451 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	452 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	453 </when>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	454 <when value='h5' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	455 <when value='homer' />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	456 <when value='ginteractions' />
21 ea19190ce5e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 iuc parents: 20 diff changeset	457 <when value='hicpro' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	458 </conditional>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	459 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	460 <token name="@REFERENCES@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	461
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	462 .. class:: infomark
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	463
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	464 For more information on the tools, please visit our `help site`_.
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	465
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	466 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	467
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	468 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	469
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	470 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	471 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	472 .. _help site: https://hicexplorer.readthedocs.org
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	473
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	474 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	475
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	476 <xml name="multiple_input_bams">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	477 <repeat name="input_files" title="BAM files" min="2">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	478 <param name="bamfile" type="data" format="bam" label="BAM file" />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	479 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	480 </repeat>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	481 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	482
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	483 <xml name="multiple_input_bigwigs">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	484 <repeat name="input_files" title="BigWig files" min="2">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	485 <param name="bigwigfile" type="data" format="bigwig" label="Bigwig file" />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	486 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead.">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	487 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	488 </param>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	489 </repeat>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	490 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	491
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	492 <xml name="plotTitle">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	493 <param name="plotTitle" type="text" value="" optional="True" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. (--plotTitle)">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	494 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	495 </param>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	496 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	497
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	498 <token name="@multiple_input_bams@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	499 #import tempfile
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	500 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	501 #set files=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	502 #set labels=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	503 #for $i in $input_files:
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	504 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	505 #set $temp_input_path = $temp_input_handle.name
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	506 #silent $temp_input_handle.close()
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	507 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	508 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	509 #silent $files.append('%s.bam' % $temp_input_path)
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	510
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	511 ##set $files += [str($i.bamfile)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	512 #if str($i.label.value) != "":
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	513 #set $labels += ["\"%s\"" % ($i.label.value)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	514 #else
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	515 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	516 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	517 #end for
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	518 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	519
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	520 <token name="@multiple_input_bigwigs@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	521 #import tempfile
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	522 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	523 #set files=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	524 #set labels=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	525 #for $i in $input_files:
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	526 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	527 #set $temp_input_path = $temp_input_handle.name
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	528 #silent $temp_input_handle.close()
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	529 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	530 #silent $files.append('%s.bw' % $temp_input_path)
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	531
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	532 ##set $files += [str($i.bigwigfile)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	533 #if str($i.label.value) != "":
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	534 #set $labels += ["\"%s\"" % ($i.label.value)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	535 #else
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	536 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	537 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	538 #end for
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	539 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	540
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	541 <xml name="reference_genome_source">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	542 <conditional name="source">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	543 <param name="ref_source" type="select" label="Reference genome">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	544 <option value="cached">locally cached</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	545 <option value="history">in your history</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	546 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	547 <when value="cached">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	548 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	549 <options from_data_table="deepTools_seqs">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	550 <filter type="sort_by" column="1" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	551 <validator type="no_options" message="No indexes are available." />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	552 </options>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	553 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	554 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	555 <when value="history">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	556 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	557 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	558 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	559 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	560
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	561 <token name="@reference_genome_source@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	562 #if $source.ref_source=="history":
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	563 --genome $source.input1
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	564 #else:
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	565 --genome "${source.input1_2bit.fields.path}"
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	566 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	567 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	568
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	569 <xml name="effectiveGenomeSize">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	570 <conditional name="effectiveGenomeSize">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	571 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" 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.
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	572 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	573 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.">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	574 <option value="93260000">ce10 (93260000)</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	575 <option value="121400000">dm3 (121400000)</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	576 <option value="2451960000" selected="true">hg19 (2451960000)</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	577 <option value="2150570000">mm9 (2150570000)</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	578 <option value="specific">user specified</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	579 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	580 <when value="specific">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	581 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	582 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	583 <when value="2150570000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	584 <when value="2451960000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	585 <when value="121400000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	586 <when value="93260000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	587 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	588 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	589
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	590 <xml name="image_file_format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	591 <param name="outFileFormat" type="select" label="Image file format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	592 <option value="png" selected="true">png</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	593 <option value="pdf">pdf</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	594 <option value="svg">svg</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	595 <option value="eps">eps</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	596 <option value="emf">emf</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	597 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	598 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	599
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	600 <xml name="missingDataAsZero">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	601 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Treat missing data as zero" 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." />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	602 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	603
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	604 <xml name="input_save_matrix_values">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	605 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	606 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	607
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	608 <xml name="input_graphic_output_settings">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	609 <conditional name="output">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	610 <param name="showOutputSettings" type="select" label="Show advanced output settings">
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	611 <option value="no" selected="true">no</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	612 <option value="yes">yes</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	613 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	614 <when value="no" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	615 <when value="yes">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	616 <yield />
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	617 <param name="saveData" type="boolean" label="Save the data underlying the average profile" />
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	618 <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." />
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	619 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	620 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	621 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	622
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	623 <xml name="input_image_file_format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	624 <param name="outFileFormat" type="select" label="Image file format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	625 <option value="png" selected="true">png</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	626 <option value="pdf">pdf</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	627 <option value="svg">svg</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	628 <option value="eps">eps</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	629 <option value="emf">emf</option>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	630 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	631 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	632
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	633 <xml name="output_image_file_format">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	634 <data format="png" name="outFileName" label="${tool.name} image">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	635 <change_format>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	636 <when input="output.outFileFormat" value="pdf" format="pdf" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	637 <when input="output.outFileFormat" value="svg" format="svg" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	638 <when input="output.outFileFormat" value="eps" format="eps" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	639 <when input="output.outFileFormat" value="emf" format="emf" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	640 </change_format>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	641 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	642 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	643
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	644 <xml name="output_save_matrix_values">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	645 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	646 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	647 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	648 output['showOutputSettings'] == 'yes' and
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	649 output['saveMatrix'] is True
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	650 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	651 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	652 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	653 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	654
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	655 <xml name="output_graphic_outputs">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	656 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	657 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	658 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	659 output['showOutputSettings'] == 'yes' and
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	660 output['saveData'] is True
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	661 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	662 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	663 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	664 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	665 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	666 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	667 output['showOutputSettings'] == 'yes' and
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	668 output['saveSortedRegions'] is True
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	669 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	670 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	671 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	672 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	673
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	674 <xml name="track_input_h5_macro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	675 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" />
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	676 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	677 <xml name="track_input_bed_macro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	678 <param name="track_input_bed" type="data" format="bed" label="Track file BED format" />
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	679 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	680 <xml name="track_input_bedgraph_macro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	681 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" />
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	682 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	683 <xml name="track_input_bigwig_macro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	684 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" />
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	685 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	686 <xml name="track_input_bedgraph_matrix_macro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	687 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" />
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	688 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	689 <xml name="track_input_tabular_macro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	690 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" />
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	691 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	692 <xml name="plot_title">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	693 <param name="title" type="text" optional="true" label="Plot title">
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	694 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	695 </param>
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	696 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	697
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	698 <xml name="spacer_macro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	699 <param name="spacer_width" type="float" value="" min="0" optional="True" label="Include spacer at the end of the track" help="Width of the spacer." />
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	700 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	701 <xml name="fontsize_macro">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	702 <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" />
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	703 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	704 </macros>

Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

annotate macros.xml @ 21:ea19190ce5e0 draft