hicexplorer_hiccorrectmatrix: macros.xml annotate

annotate macros.xml @ 19:e4cb7809df61 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

author	iuc
date	Tue, 16 Mar 2021 15:41:08 +0000
parents	5443b2b1165f
children	f5a37c3906cc

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>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	3 <token name="@TOOL_VERSION@">3.6</token>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 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>
6 3889ecd44f20 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058 iuc parents: 5 diff changeset	40 <citation type="doi">10.5281/zenodo.1133705</citation>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	41 <yield />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	42 </citations>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	43 </xml>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	44 <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	45 <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	46 </xml>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	47
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	48 <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	49 <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	50 (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	51 </xml>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	52
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	53 <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	54 <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	55 "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	56 <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	57 </param>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	58 </xml>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	59 <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	60 <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	61 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	62 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	63 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	64 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	65 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	66 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	67 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	68 <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	69 </param>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	70 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	71
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	72 <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	73 <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	74 <!-- 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	75 </xml>
8 f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	76 <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	77 <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	78 <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	79 <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	80 <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	81 </param>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	82 <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	83 <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	84 <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	85 </when>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	86 </conditional>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	87 </xml>
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	88
f7d344dacfeb planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 iuc parents: 6 diff changeset	89 <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	90 <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	91 <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	92 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	93
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	94 <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	95 <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	96 <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	97 <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	98 <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	99 <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	100 <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	101 <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	102 <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	103 <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	104 <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	105 <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	106 <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	107 <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	108 <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	109 <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	110 <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	111 <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	112 <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	113 <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	114 <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	115 <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	116 <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	117 <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	118 <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	119 <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	120 <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	121 <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	122 <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	123 <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	124 <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	125 <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	126 <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	127 <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	128 <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	129 <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	130 <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	131 <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	132 <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	133 <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	134 <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	135 <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	136 <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	137 <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	138 <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	139 <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	140 <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	141 <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	142 <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	143 <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	144 <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	145 <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	146 <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	147 <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	148 <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	149 <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	150 <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	151 <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	152 <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	153 <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	154 <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	155 <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	156 <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	157 <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	158 <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	159 <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	160 <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	161 <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	162 <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	163 <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	164 <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	165 <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	166 <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	167 <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	168 <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	169 <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	170 <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	171 <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	172 <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	173 <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	174 <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	175 <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	176 <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	177 <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	178 <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	179 <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	180 <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	181 <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	182 <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	183 <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	184 <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	185 <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	186 <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	187 <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	188 <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	189 <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	190 <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	191 <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	192 <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	193 <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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 <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	201 <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	202 <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	203 <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	204 <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	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 <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	212 <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	213 <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	214 <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	215 <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	216 <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	217 <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	218 <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	219 <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	220 <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	221 <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	222 <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	223 <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	224 <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	225 <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	226 <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	227 <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	228 <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	229 <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	230 <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	231 <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	232 <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	233 <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	234 <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	235 <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	236 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	237 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	238
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	239 <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	240 <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	241 <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	242 <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	243 </repeat>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	244 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	245
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	246 <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	247 #set $matrices = []
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	248 #set $mlabels = []
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	249 #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	250 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	251 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	252
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	253 #if str($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	254 #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	255 #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	256 #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	257 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	258 #end for
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	259 #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	260 #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	261 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	262
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	263 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	264 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($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	265 <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	266
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	267 <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	268 <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	269 <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	270 </param>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	271 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	272
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	273 <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	274 <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	275 <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	276 <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	277 <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	278 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	279 <when value="no">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	280 <conditional name="clustering">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	281 <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	282 <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	283 <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	284 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	285 <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	286 <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	287 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	288 <when value="none" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	289 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	290 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	291 <when value="yes" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	292 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	293 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	294
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	295 <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	296 #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	297 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	298 #if int($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	299 --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	300 #end if
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 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	304
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	305 <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	306 <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	307 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	308 <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	309 <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	310 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	311 <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	312 <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	313 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	314 <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	315 <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	316 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	317 <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	318 <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	319 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	320 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	321 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	322
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	323 <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	324 <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	325 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	326
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	327 <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	328 <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	329 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	330
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	331 <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	332 <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	333 <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	334 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	335 <xml name="xMax">
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	336 <param argument="--xMax" name="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	337 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	338 <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	339 <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	340 <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	341 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	342 <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	343 <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	344 </xml>
5 44919af9194b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 bgruening parents: 4 diff changeset	345 <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	346 <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	347 </xml>
44919af9194b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 bgruening parents: 4 diff changeset	348 <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	349 <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	350 </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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <option value="optionHicpro">HiCPro</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	359 </param>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 </when>
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="optionH5">
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' />
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	369 </when>
14 1e622e371512 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064" bgruening parents: 13 diff changeset	370 <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	371 <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	372 <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	373 <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	374 </param>
e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	375 </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	376 <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	377 <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	378 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	379 <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	380 <param name='matrixHicpro' type='data' format='txt' 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	381 <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	382 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	383 </conditional>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	384 </xml>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	385
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	386 <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	387 <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	388 <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	389 <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	390 <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	391 <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	392 <option value="optionHicpro">HiCPro</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	393 </param>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	394 <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	395 <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	396 <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	397 <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	398 <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	399 <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	400 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	401 <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	402 <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	403 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	404 <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	405 <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	406 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	407 <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	408 <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	409 <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	410 </when>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	411 </conditional>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	412 </xml>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	413 <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	414 <!-- <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	415 <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	416 <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	417 <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	418 <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	419 <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	420 <option value="ginteractions">ginteractions</option>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	421 </param>
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="cool">
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='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	424 <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	425 </when>
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	426 <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	427 <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	428 <when value='ginteractions' />
13 9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	429 </conditional>
9949f055db84 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty" bgruening parents: 11 diff changeset	430 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	431 <token name="@REFERENCES@">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	432
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	433 .. class:: infomark
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	434
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	435 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	436
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	437 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	438
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	439 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	440
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	441 .. _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	442 .. _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	443 .. _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	444
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	445 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	446
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	447 <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	448 <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	449 <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	450 <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	451 </repeat>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	452 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	453
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	454 <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	455 <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	456 <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	457 <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	458 <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	459 </param>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	460 </repeat>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	461 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	462
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	463 <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	464 <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	465 <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	466 </param>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	467 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	468
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	469 <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	470 #import tempfile
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	471 #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	472 #set files=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	473 #set labels=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	474 #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	475 #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	476 #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	477 #silent $temp_input_handle.close()
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	478 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	479 #silent os.system("ln -s %s %s.bam.bai" % (str($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	480 #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	481
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	482 ##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	483 #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	484 #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	485 #else
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	486 #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	487 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	488 #end for
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	489 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	490
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	491 <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	492 #import tempfile
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	493 #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	494 #set files=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	495 #set labels=[]
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	496 #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	497 #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	498 #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	499 #silent $temp_input_handle.close()
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	500 #silent os.system("ln -s %s %s.bw" % (str($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	501 #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	502
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	503 ##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	504 #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	505 #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	506 #else
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	507 #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	508 #end if
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	509 #end for
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	510 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	511
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	512 <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	513 <conditional name="source">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	514 <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	515 <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	516 <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	517 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	518 <when value="cached">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	519 <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	520 <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	521 <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	522 <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	523 </options>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	524 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	525 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	526 <when value="history">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	527 <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	528 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	529 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	530 </xml>
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 <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	533 #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	534 --genome $source.input1
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	535 #else:
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	536 --genome "${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	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 </token>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	539
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	540 <xml name="effectiveGenomeSize">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	541 <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	542 <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	543 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	544 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	545 <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	546 <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	547 <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	548 <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	549 <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	550 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	551 <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	552 <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	553 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	554 <when value="2150570000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	555 <when value="2451960000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	556 <when value="121400000" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	557 <when value="93260000" />
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 <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	562 <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	563 <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	564 <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	565 <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	566 <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	567 <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	568 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	569 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	570
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	571 <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	572 <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	573 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	574
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	575 <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	576 <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	577 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	578
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	579 <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	580 <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	581 <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	582 <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	583 <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	584 </param>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	585 <when value="no" />
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	586 <when value="yes">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	587 <yield />
19 e4cb7809df61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f" iuc parents: 18 diff changeset	588 <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	589 <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	590 </when>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	591 </conditional>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	592 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	593
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	594 <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	595 <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	596 <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	597 <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	598 <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	599 <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	600 <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	601 </param>
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="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	605 <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	606 <change_format>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	607 <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	608 <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	609 <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	610 <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	611 </change_format>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	612 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	613 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	614
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	615 <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	616 <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	617 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	618 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	619 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	620 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	621 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	622 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	623 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	624 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	625
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	626 <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	627 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	628 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	629 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	630 output['showOutputSettings'] == 'yes' and
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	631 output['saveData'] is True
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	632 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	633 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	634 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	635 <data format="bed" name="outFileSortedRegions" label="${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	636 <filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	637 ((
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	638 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	639 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	640 ))
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	641 </filter>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	642 </data>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	643 </xml>
d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	644
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	645 <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	646 <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	647 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	648 <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	649 <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	650 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	651 <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	652 <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	653 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	654 <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	655 <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	656 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	657 <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	658 <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	659 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	660 <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	661 <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	662 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	663 <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	664 <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	665 <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	666 </param>
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	667 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	668
2 ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	669 <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	670 <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	671 </xml>
ecf11dda45f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 bgruening parents: 1 diff changeset	672 <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	673 <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	674 </xml>
0 d5bf8c60d661 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 bgruening parents: diff changeset	675 </macros>

Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

annotate macros.xml @ 19:e4cb7809df61 draft