hicexplorer_hictraintadclassifier: macros.xml annotate

annotate macros.xml @ 0:1ff19476c5a5 draft default tip

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

author	bgruening
date	Wed, 18 Oct 2023 16:22:57 +0000
parents
children

rev	line source
0 1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	1 <macros>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	3 <token name="@TOOL_VERSION@">3.7.2</token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	4 <token name="@VERSION_SUFFIX@">0</token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	5 <token name="@USE_RANGE@">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	6 #if $use_range.select_use_range == "yes_use_range":
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	7 --range $use_range.range_min:$use_range.range_max
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	8 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	9 </token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	10
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	11 <xml name="requirements">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	12 <requirements>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	13 <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	14 <yield />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	15 </requirements>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	16 <version_command>@BINARY@ --version</version_command>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	17 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	18
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	19 <token name="@CHROMOSOME_LIST@">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	20 #if $chromosome_list:
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	21 #set $chromosomes = []
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	22 #for $chrom in $chromosome_list:
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	23 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	24 #end for
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	25 #set $chromosome_string = ' '.join($chromosomes)
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	26 --chromosomes $chromosome_string
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	27 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	28 </token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	29
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	30 <xml name="chromosome_list">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: 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.">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	32 <param argument="--chromosomes" type="text" value="">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	33 <validator type="empty_field" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	34 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	35 </repeat>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	36 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	37
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	38 <xml name="citations">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	39 <citations>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	40 <citation type="doi">10.1093/nar/gkaa220</citation>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	41 <citation type="doi">10.1093/nar/gky504</citation>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	42 <yield />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	43 </citations>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	44 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	45 <xml name="dpi">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	46 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	47 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	48
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	49 <xml name="restrictionCutFile">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	50 <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	51 (i.e. the region between one restriction site and the next)." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	52 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	53
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	54 <xml name="restrictionSequence">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	55 <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	56 "dangling-ends". If not given, such statistics will not be available.">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	57 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	58 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	59 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	60 <xml name="danglingSequence">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	61 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	62 Each restriction enzyme recognizes a different DNA sequence and,
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	63 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	64 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	65 For DpnII, the restriction site and dangling end sequence are the same: GATC.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	66 This information is easily found on the description of the restriction enzyme.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	67 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	68 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	69 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	70 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	71 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	72
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	73 <xml name="zMax">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	74 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	75 <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	76 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	77 <xml name="use_range">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	78 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	79 <param name="select_use_range" argument="--range" type="select" label="Range restriction (in bp)" help="If given, only counts within the specified range are considered.">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	80 <option value="no_use_range">No restriction</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	81 <option value="yes_use_range">Only consider counts within a range</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	82 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	83 <when value="no_use_range" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	84 <when value="yes_use_range">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	85 <expand macro='range' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	86 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	87 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	88 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	89
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	90 <xml name="range">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	91 <param name='range_min' type="integer" value="" min="0" label="Minimum range to consider interactions" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	92 <param name='range_max' type="integer" value="" min="0" label="Maximum range to consider interactions" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	93 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	94
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	95 <xml name="colormap">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	96 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	97 <option value="RdYlBu">RdYlBu</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	98 <option value="Accent">Accent</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	99 <option value="Spectral">Spectral</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	100 <option value="Set1">Set1</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	101 <option value="Set2">Set2</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	102 <option value="Set3">Set3</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	103 <option value="Dark2">Dark2</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	104 <option value="Reds">Reds</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	105 <option value="Oranges">Oranges</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	106 <option value="Greens">Greens</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	107 <option value="Blues">Blues</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	108 <option value="Greys">Greys</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	109 <option value="Purples">Purples</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	110 <option value="Paired">Paired</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	111 <option value="Pastel1">Pastel1</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	112 <option value="Pastel2">Pastel2</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	113 <option value="spring">spring</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	114 <option value="summer">summer</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	115 <option value="autumn">autumn</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	116 <option value="winter">winter</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	117 <option value="hot">hot</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	118 <option value="coolwarm">coolwarm</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	119 <option value="cool">cool</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	120 <option value="seismic">seismic</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	121 <option value="terrain">terrain</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	122 <option value="ocean">ocean</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	123 <option value="rainbow">rainbow</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	124 <option value="bone">bone</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	125 <option value="flag">flag</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	126 <option value="prism">prism</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	127 <option value="cubehelix">cubehelix</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	128 <option value="binary">binary</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	129 <option value="pink">pink</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	130 <option value="gray">gray</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	131 <option value="copper">copper</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	132 <option value="BrBG">BrBG</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	133 <option value="BuGn">BuGn</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	134 <option value="BuPu">BuPu</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	135 <option value="GnBu">GnBu</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	136 <option value="OrRd">OrRd</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	137 <option value="PiYG">PiYG</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	138 <option value="PRGn">PRGn</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	139 <option value="PuOr">PuOr</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	140 <option value="PuRd">PuRd</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	141 <option value="PuBu">PuBu</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	142 <option value="RdBu">RdBu</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	143 <option value="RdGy">RdGy</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	144 <option value="RdPu">RdPu</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	145 <option value="YlGn">YlGn</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	146 <option value="PuBuGn">PuBuGn</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	147 <option value="RdYlGn">RdYlGn</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	148 <option value="YlGnBu">YlGnBu</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	149 <option value="YlOrBr">YlOrBr</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	150 <option value="YlOrRd">YlOrRd</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	151 <option value="gist_gray">gist_gray</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	152 <option value="gist_stern">gist_stern</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	153 <option value="gist_earth">gist_earth</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	154 <option value="gist_yarg">gist_yarg</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	155 <option value="gist_ncar">gist_ncar</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	156 <option value="gist_rainbow">gist_rainbow</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	157 <option value="gist_heat">gist_heat</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	158 <option value="gnuplot">gnuplot</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	159 <option value="gnuplot2">gnuplot2</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	160 <option value="CMRmap">CMRmap</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	161 <option value="bwr">bwr</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	162 <option value="hsv">hsv</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	163 <option value="brg">brg</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	164 <option value="jet">jet</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	165 <option value="afmhot">afmhot</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	166 <option value="plasma">plasma</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	167 <option value="Accent_r">Accent reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	168 <option value="Spectral_r">Spectral reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	169 <option value="Set1_r">Set1 reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	170 <option value="Set2_r">Set2 reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	171 <option value="Set3_r">Set3 reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	172 <option value="Dark2_r">Dark2 reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	173 <option value="Reds_r">Reds reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	174 <option value="Oranges_r">Oranges reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	175 <option value="Greens_r">Greens reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	176 <option value="Blues_r">Blues reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	177 <option value="Greys_r">Greys reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	178 <option value="Purples_r">Purples reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	179 <option value="Paired_r">Paired reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	180 <option value="Pastel1_r">Pastel1 reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	181 <option value="Pastel2_r">Pastel2 reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	182 <option value="spring_r">spring reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	183 <option value="summer_r">summer reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	184 <option value="autumn_r">autumn reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	185 <option value="winter_r">winter reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	186 <option value="hot_r">hot reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	187 <option value="coolwarm_r">coolwarm reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	188 <option value="cool_r">cool reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	189 <option value="seismic_r">seismic reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	190 <option value="terrain_r">terrain reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	191 <option value="ocean_r">ocean reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	192 <option value="rainbow_r">rainbow reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	193 <option value="bone_r">bone reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	194 <option value="flag_r">flag reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	195 <option value="prism_r">prism reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	196 <option value="cubehelix_r">cubehelix reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	197 <option value="binary_r">binary reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	198 <option value="pink_r">pink reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	199 <option value="gray_r">gray reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	200 <option value="copper_r">copper reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	201 <option value="BrBG_r">BrBG reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	202 <option value="BuGn_r">BuGn reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	203 <option value="BuPu_r">BuPu reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	204 <option value="GnBu_r">GnBu reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	205 <option value="OrRd_r">OrRd reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	206 <option value="PiYG_r">PiYG reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	207 <option value="PRGn_r">PRGn reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	208 <option value="PuOr_r">PuOr reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	209 <option value="PuRd_r">PuRd reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	210 <option value="PuBu_r">PuBu reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	211 <option value="RdBu_r">RdBu reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	212 <option value="RdGy_r">RdGy reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	213 <option value="RdPu_r">RdPu reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	214 <option value="YlGn_r">YlGn reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	215 <option value="PuBuGn_r">PuBuGn reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	216 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	217 <option value="RdYlGn_r">RdYlGn reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	218 <option value="YlGnBu_r">YlGnBu reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	219 <option value="YlOrBr_r">YlOrBr reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	220 <option value="YlOrRd_r">YlOrRd reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	221 <option value="gist_gray_r">gist_gray reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	222 <option value="gist_stern_r">gist_stern reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	223 <option value="gist_earth_r">gist_earth reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	224 <option value="gist_yarg_r">gist_yarg reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	225 <option value="gist_ncar_r">gist_ncar reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	226 <option value="gist_rainbow_r">gist_rainbow reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	227 <option value="gist_heat_r">gist_heat reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	228 <option value="gnuplot_r">gnuplot reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	229 <option value="gnuplot2_r">gnuplot2 reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	230 <option value="CMRmap_r">CMRmap reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	231 <option value="bwr_r">bwr reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	232 <option value="hsv_r">hsv reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	233 <option value="brg_r">brg reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	234 <option value="jet_r">jet reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	235 <option value="afmhot_r">afmhot reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	236 <option value="plasma_r">plasma reversed</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	237 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	238 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	239
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	240 <xml name="multiple_input_matrices">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	241 <repeat name="input_files" title="Hi-C Matrix files" min="2">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	242 <param name="matrix" type="data" format="h5,cool" label="Hi-C Matrix file" help="" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	243 <param name="mlabel" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	244 </repeat>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	245 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	246
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	247 <token name="@multiple_input_matrices@">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	248 #set $matrices = []
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	249 #set $mlabels = []
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	250 #for $counter, $i in enumerate($input_files):
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	251 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	252 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	253
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	254 #if str($i.mlabel.value) != "":
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	255 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	256 #else
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	257 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	258 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	259 #end for
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	260 #set $mlabels = ' '.join($mlabels)
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	261 #set $matrices = ' '.join($matrices)
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	262 </token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	263
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	264 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	265 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	266 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	267
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	268 <xml name="region">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	269 <param argument="--region" type="text" label="Region of the genome to limit the operation" help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	270 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	271 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	272 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	273
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	274 <xml name="kmeans_clustering">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	275 <conditional name="used_multiple_regions">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	276 <param name="used_multiple_regions_options" type="select" label="Did you compute the matrix with more than one groups of regions?" help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	277 <option value="yes">Yes, I used multiple groups of regions</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	278 <option value="no">No, I used only one group</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	279 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	280 <when value="no">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	281 <conditional name="clustering">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	282 <param name="clustering_options" type="select" label="Clustering algorithm">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	283 <option value="none">No clustering</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	284 <option value="kmeans">Kmeans clustering</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	285 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	286 <when value="kmeans">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	287 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	288 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	289 <when value="none" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	290 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	291 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	292 <when value="yes" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	293 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	294 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	295
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	296 <token name="@KMEANS_CLUSTERING@">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	297 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	298 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	299 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	300 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	301 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	302 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	303 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	304 </token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	305
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	306 <xml name="samFlag">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	307 <param name="samFlag" type="integer" optional="true" value="" label="Filter reads based on the SAM flag" help="For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	308 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	309 <xml name="plotNumbers">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	310 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" label="Plot the correlation value" help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	311 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	312 <xml name="doNotExtendPairedEnds">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	313 <param argument="--doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" label="Do not extend paired ends" help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	314 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	315 <xml name="ignoreDuplicates">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	316 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" label="Ignore duplicates" help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	317 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	318 <xml name="minMappingQuality">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	319 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" label="Minimum mapping quality" help= "If set, only reads that have a mapping quality score higher than the given value are considered.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	320 Note Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	321 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	322 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	323
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	324 <xml name="skipZeros">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	325 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label="Skip zeros" help="If set, then zero counts that happen for all BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	326 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	327
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	328 <xml name="fragmentLength">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	329 <param argument="--fragmentLength" type="integer" value="300" min="1" label="Fragment length used for the sequencing" help="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	330 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	331
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	332 <xml name="scaleFactor">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	333 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	334 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	335 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	336 <xml name="xMax">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	337 <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	338 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	339 <xml name="filterThreshold">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	340 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	341 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	342 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	343 <xml name="pseudocount">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	344 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	345 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	346 <xml name='matrix_h5_cooler_macro'>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	347 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	348 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	349 <xml name='matrix_h5_cooler_multiple_macro'>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	350 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	351 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	352
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	353 <xml name='matrix_cooler_multiple_macro'>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	354 <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	355 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	356 <xml name='convertFormat_single_macro'>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	357 <conditional name="inputFormat_conditional">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	358 <param name="inputFormat_selector" type="select" label="Choose input file type">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	359 <option value="optionCool" selected="True">cool</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	360 <option value="optionH5">h5</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	361 <option value="optionHic">hic</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	362 <option value="optionHomer">Homer</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	363 <option value="optionHicpro">HiCPro</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	364 <option value="option2Dtext">2D-text</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	365
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	366 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	367 <when value="optionCool">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	368 <expand macro='matrix_h5_cooler_macro' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	369 <param name='correctionName' type='text' label='Correction factors column name' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	370 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	371 <param name='chromosome' type='text' label='Load only one chromosome' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	372 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	373 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	374 <when value="optionH5">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	375 <expand macro='matrix_h5_cooler_macro' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	376 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	377 <when value="optionHic">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	378 <param name='matrixHic' type='data' format='hic' label='.hic matrix' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	379 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	380 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	381 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	382 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	383 <when value="optionHomer">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	384 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	385 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	386 <when value="optionHicpro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	387 <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	388 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	389 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	390 <when value="option2Dtext">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	391 <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	392
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	393 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	394 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	395 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	396 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	397 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	398 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	399 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	400
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	401 <xml name='convertFormat_multiple_macro'>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	402 <conditional name="inputFormat_conditional">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	403 <param name="inputFormat_selector" type="select" label="Choose input file type">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	404 <option value="optionCool" selected="True">cool</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	405 <option value="optionH5">h5</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	406 <option value="optionHomer">Homer</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	407 <option value="optionHicpro">HiCPro</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	408 <option value="option2Dtext">2D-text</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	409
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	410
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	411 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	412 <when value="optionCool">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	413 <expand macro='matrix_h5_cooler_multiple_macro' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	414 <param name='correctionName' type='text' label='Correction factors column name' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	415 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	416 <param name='chromosome' type='text' label='Load only one chromosome' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	417 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	418 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	419 <when value="optionH5">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	420 <expand macro='matrix_h5_cooler_multiple_macro' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	421 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	422 <when value="optionHomer">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	423 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	424 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	425 <when value="optionHicpro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	426 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	427 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	428 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	429 <when value="option2Dtext">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	430 <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	431
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	432 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	433 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	434 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	435 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	436 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	437 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	438 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	439 <xml name='convertFormat_single_output_macro'>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	440 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	441 <conditional name="outputFormat_conditional">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	442 <param name="outputFormat_selector" type="select" label="Choose output file type">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	443 <option value="cool" selected="True">cool</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	444 <option value="h5">h5</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	445 <option value="homer">Homer</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	446 <option value="ginteractions">ginteractions</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	447 <option value="hicpro">hicpro</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	448
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	449 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	450 <when value="cool">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	451 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	452 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	453 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	454 <when value='h5' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	455 <when value='homer' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	456 <when value='ginteractions' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	457 <when value='hicpro' />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	458 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	459 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	460 <token name="@REFERENCES@">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	461
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	462 .. class:: infomark
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	463
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	464 For more information on the tools, please visit our `help site`_.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	465
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	466 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	467
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	468 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	469
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	470 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	471 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	472 .. _help site: https://hicexplorer.readthedocs.org
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	473
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	474 </token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	475
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	476 <xml name="multiple_input_bams">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	477 <repeat name="input_files" title="BAM files" min="2">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	478 <param name="bamfile" type="data" format="bam" label="BAM file" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	479 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	480 </repeat>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	481 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	482
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	483 <xml name="multiple_input_bigwigs">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	484 <repeat name="input_files" title="BigWig files" min="2">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	485 <param name="bigwigfile" type="data" format="bigwig" label="Bigwig file" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	486 <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead.">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	487 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	488 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	489 </repeat>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	490 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	491
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	492 <xml name="plotTitle">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	493 <param name="plotTitle" type="text" value="" optional="True" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. (--plotTitle)">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	494 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	495 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	496 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	497
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	498 <token name="@multiple_input_bams@">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	499 #import tempfile
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	500 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	501 #set files=[]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	502 #set labels=[]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	503 #for $i in $input_files:
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	504 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	505 #set $temp_input_path = $temp_input_handle.name
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	506 #silent $temp_input_handle.close()
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	507 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	508 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	509 #silent $files.append('%s.bam' % $temp_input_path)
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	510
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	511 ##set $files += [str($i.bamfile)]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	512 #if str($i.label.value) != "":
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	513 #set $labels += ["\"%s\"" % ($i.label.value)]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	514 #else
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	515 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	516 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	517 #end for
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	518 </token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	519
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	520 <token name="@multiple_input_bigwigs@">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	521 #import tempfile
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	522 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	523 #set files=[]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	524 #set labels=[]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	525 #for $i in $input_files:
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	526 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	527 #set $temp_input_path = $temp_input_handle.name
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	528 #silent $temp_input_handle.close()
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	529 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	530 #silent $files.append('%s.bw' % $temp_input_path)
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	531
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	532 ##set $files += [str($i.bigwigfile)]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	533 #if str($i.label.value) != "":
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	534 #set $labels += ["\"%s\"" % ($i.label.value)]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	535 #else
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	536 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	537 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	538 #end for
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	539 </token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	540
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	541 <xml name="reference_genome_source">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	542 <conditional name="source">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	543 <param name="ref_source" type="select" label="Reference genome">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	544 <option value="cached">locally cached</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	545 <option value="history">in your history</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	546 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	547 <when value="cached">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	548 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	549 <options from_data_table="deepTools_seqs">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	550 <filter type="sort_by" column="1" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	551 <validator type="no_options" message="No indexes are available." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	552 </options>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	553 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	554 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	555 <when value="history">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	556 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	557 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	558 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	559 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	560
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	561 <token name="@reference_genome_source@">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	562 #if $source.ref_source=="history":
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	563 --genome $source.input1
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	564 #else:
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	565 --genome "${source.input1_2bit.fields.path}"
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	566 #end if
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	567 </token>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	568
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	569 <xml name="effectiveGenomeSize">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	570 <conditional name="effectiveGenomeSize">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	571 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	572 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	573 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	574 <option value="93260000">ce10 (93260000)</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	575 <option value="121400000">dm3 (121400000)</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	576 <option value="2451960000" selected="true">hg19 (2451960000)</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	577 <option value="2150570000">mm9 (2150570000)</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	578 <option value="specific">user specified</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	579 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	580 <when value="specific">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	581 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	582 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	583 <when value="2150570000" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	584 <when value="2451960000" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	585 <when value="121400000" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	586 <when value="93260000" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	587 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	588 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	589
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	590 <xml name="image_file_format">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	591 <param name="outFileFormat" type="select" label="Image file format">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	592 <option value="png" selected="true">png</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	593 <option value="pdf">pdf</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	594 <option value="svg">svg</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	595 <option value="eps">eps</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	596 <option value="emf">emf</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	597 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	598 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	599
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	600 <xml name="missingDataAsZero">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	601 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Treat missing data as zero" help="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	602 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	603
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	604 <xml name="input_save_matrix_values">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	605 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	606 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	607
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	608 <xml name="input_graphic_output_settings">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	609 <conditional name="output">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	610 <param name="showOutputSettings" type="select" label="Show advanced output settings">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	611 <option value="no" selected="true">no</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	612 <option value="yes">yes</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	613 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	614 <when value="no" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	615 <when value="yes">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	616 <yield />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	617 <param name="saveData" type="boolean" label="Save the data underlying the average profile" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	618 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	619 </when>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	620 </conditional>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	621 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	622
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	623 <xml name="input_image_file_format">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	624 <param name="outFileFormat" type="select" label="Image file format">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	625 <option value="png" selected="true">png</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	626 <option value="pdf">pdf</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	627 <option value="svg">svg</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	628 <option value="eps">eps</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	629 <option value="emf">emf</option>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	630 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	631 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	632
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	633 <xml name="output_image_file_format">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	634 <data format="png" name="outFileName" label="${tool.name} image">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	635 <change_format>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	636 <when input="output.outFileFormat" value="pdf" format="pdf" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	637 <when input="output.outFileFormat" value="svg" format="svg" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	638 <when input="output.outFileFormat" value="eps" format="eps" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	639 <when input="output.outFileFormat" value="emf" format="emf" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	640 </change_format>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	641 </data>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	642 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	643
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	644 <xml name="output_save_matrix_values">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	645 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	646 <filter>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	647 ((
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	648 output['showOutputSettings'] == 'yes' and
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	649 output['saveMatrix'] is True
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	650 ))
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	651 </filter>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	652 </data>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	653 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	654
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	655 <xml name="output_graphic_outputs">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	656 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	657 <filter>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	658 ((
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	659 output['showOutputSettings'] == 'yes' and
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	660 output['saveData'] is True
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	661 ))
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	662 </filter>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	663 </data>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	664 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	665 <filter>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	666 ((
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	667 output['showOutputSettings'] == 'yes' and
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	668 output['saveSortedRegions'] is True
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	669 ))
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	670 </filter>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	671 </data>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	672 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	673
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	674 <xml name="track_input_h5_macro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	675 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	676 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	677 <xml name="track_input_bed_macro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	678 <param name="track_input_bed" type="data" format="bed" label="Track file BED format" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	679 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	680 <xml name="track_input_bedgraph_macro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	681 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	682 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	683 <xml name="track_input_bigwig_macro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	684 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	685 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	686 <xml name="track_input_bedgraph_matrix_macro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	687 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	688 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	689 <xml name="track_input_tabular_macro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	690 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	691 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	692 <xml name="plot_title">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	693 <param name="title" type="text" optional="true" label="Plot title">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	694 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	695 </param>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	696 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	697
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	698 <xml name="spacer_macro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	699 <param name="spacer_width" type="float" value="" min="0" optional="True" label="Include spacer at the end of the track" help="Width of the spacer." />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	700 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	701 <xml name="fontsize_macro">
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	702 <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" />
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	703 </xml>
1ff19476c5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9 bgruening parents: diff changeset	704 </macros>

Mercurial > repos > bgruening > hicexplorer_hictraintadclassifier

annotate macros.xml @ 0:1ff19476c5a5 draft default tip