Mercurial > repos > bgruening > hicexplorer_hicmergedomains
annotate macros.xml @ 3:b6b8c8672756 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author | iuc |
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date | Mon, 01 Jul 2024 19:27:36 +0000 |
parents | b376ef118807 |
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6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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1 <macros> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> |
3
b6b8c8672756
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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3 <token name="@TOOL_VERSION@">3.7.5</token> |
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b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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4 <token name="@VERSION_SUFFIX@">0</token> |
3
b6b8c8672756
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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5 <token name="@PROFILE@">23.0</token> |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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6 <token name="@USE_RANGE@"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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7 #if $use_range.select_use_range == "yes_use_range": |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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8 --range $use_range.range_min:$use_range.range_max |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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9 #end if |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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10 </token> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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11 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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12 <xml name="requirements"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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13 <requirements> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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14 <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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15 <yield /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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16 </requirements> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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17 <version_command>@BINARY@ --version</version_command> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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18 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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19 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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20 <token name="@CHROMOSOME_LIST@"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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21 #if $chromosome_list: |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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22 #set $chromosomes = [] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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23 #for $chrom in $chromosome_list: |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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24 #silent $chromosomes.append("'%s'" % $chrom.chromosomes) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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25 #end for |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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26 #set $chromosome_string = ' '.join($chromosomes) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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27 --chromosomes $chromosome_string |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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28 #end if |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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29 </token> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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30 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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31 <xml name="chromosome_list"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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32 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included."> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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33 <param argument="--chromosomes" type="text" value=""> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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34 <validator type="empty_field" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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35 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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36 </repeat> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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37 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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38 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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39 <xml name="citations"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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40 <citations> |
2
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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41 <citation type="doi">10.1093/nar/gkaa220</citation> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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42 <citation type="doi">10.1093/nar/gky504</citation> |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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43 <yield /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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44 </citations> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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45 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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46 <xml name="dpi"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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47 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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48 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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49 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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50 <xml name="restrictionCutFile"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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51 <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 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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52 (i.e. the region between one restriction site and the next)." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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53 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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54 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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55 <xml name="restrictionSequence"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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56 <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 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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57 "dangling-ends". If not given, such statistics will not be available."> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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58 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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59 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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60 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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61 <xml name="danglingSequence"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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62 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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63 Each restriction enzyme recognizes a different DNA sequence and, |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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64 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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65 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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66 For DpnII, the restriction site and dangling end sequence are the same: GATC. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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67 This information is easily found on the description of the restriction enzyme. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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68 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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69 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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70 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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71 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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72 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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73 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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74 <xml name="zMax"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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75 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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76 <!-- this should only be enabled when both or 3d is selected for param whatToShow --> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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77 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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78 <xml name="use_range"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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79 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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80 <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."> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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81 <option value="no_use_range">No restriction</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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82 <option value="yes_use_range">Only consider counts within a range</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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83 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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84 <when value="no_use_range" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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85 <when value="yes_use_range"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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86 <expand macro='range' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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87 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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88 </conditional> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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89 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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90 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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91 <xml name="range"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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92 <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." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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93 <param name='range_max' type="integer" value="" min="0" label="Maximum range to consider interactions" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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94 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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95 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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96 <xml name="colormap"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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97 <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"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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98 <option value="RdYlBu">RdYlBu</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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99 <option value="Accent">Accent</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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100 <option value="Spectral">Spectral</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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101 <option value="Set1">Set1</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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102 <option value="Set2">Set2</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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103 <option value="Set3">Set3</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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104 <option value="Dark2">Dark2</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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105 <option value="Reds">Reds</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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106 <option value="Oranges">Oranges</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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107 <option value="Greens">Greens</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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108 <option value="Blues">Blues</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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109 <option value="Greys">Greys</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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110 <option value="Purples">Purples</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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111 <option value="Paired">Paired</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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112 <option value="Pastel1">Pastel1</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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113 <option value="Pastel2">Pastel2</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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114 <option value="spring">spring</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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115 <option value="summer">summer</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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116 <option value="autumn">autumn</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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117 <option value="winter">winter</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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118 <option value="hot">hot</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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119 <option value="coolwarm">coolwarm</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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120 <option value="cool">cool</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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121 <option value="seismic">seismic</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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122 <option value="terrain">terrain</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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123 <option value="ocean">ocean</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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124 <option value="rainbow">rainbow</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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125 <option value="bone">bone</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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126 <option value="flag">flag</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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127 <option value="prism">prism</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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128 <option value="cubehelix">cubehelix</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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129 <option value="binary">binary</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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130 <option value="pink">pink</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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131 <option value="gray">gray</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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132 <option value="copper">copper</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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133 <option value="BrBG">BrBG</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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134 <option value="BuGn">BuGn</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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135 <option value="BuPu">BuPu</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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136 <option value="GnBu">GnBu</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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137 <option value="OrRd">OrRd</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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138 <option value="PiYG">PiYG</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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139 <option value="PRGn">PRGn</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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140 <option value="PuOr">PuOr</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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141 <option value="PuRd">PuRd</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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142 <option value="PuBu">PuBu</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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143 <option value="RdBu">RdBu</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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144 <option value="RdGy">RdGy</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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145 <option value="RdPu">RdPu</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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146 <option value="YlGn">YlGn</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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147 <option value="PuBuGn">PuBuGn</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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148 <option value="RdYlGn">RdYlGn</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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149 <option value="YlGnBu">YlGnBu</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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150 <option value="YlOrBr">YlOrBr</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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151 <option value="YlOrRd">YlOrRd</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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152 <option value="gist_gray">gist_gray</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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153 <option value="gist_stern">gist_stern</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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154 <option value="gist_earth">gist_earth</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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155 <option value="gist_yarg">gist_yarg</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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156 <option value="gist_ncar">gist_ncar</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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157 <option value="gist_rainbow">gist_rainbow</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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158 <option value="gist_heat">gist_heat</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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159 <option value="gnuplot">gnuplot</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
160 <option value="gnuplot2">gnuplot2</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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parents:
diff
changeset
|
161 <option value="CMRmap">CMRmap</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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parents:
diff
changeset
|
162 <option value="bwr">bwr</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
163 <option value="hsv">hsv</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
164 <option value="brg">brg</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
165 <option value="jet">jet</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
166 <option value="afmhot">afmhot</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
167 <option value="plasma">plasma</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
168 <option value="Accent_r">Accent reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
169 <option value="Spectral_r">Spectral reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
170 <option value="Set1_r">Set1 reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
171 <option value="Set2_r">Set2 reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
172 <option value="Set3_r">Set3 reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
173 <option value="Dark2_r">Dark2 reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
174 <option value="Reds_r">Reds reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
175 <option value="Oranges_r">Oranges reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
176 <option value="Greens_r">Greens reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
177 <option value="Blues_r">Blues reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
178 <option value="Greys_r">Greys reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
179 <option value="Purples_r">Purples reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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parents:
diff
changeset
|
180 <option value="Paired_r">Paired reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
181 <option value="Pastel1_r">Pastel1 reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
182 <option value="Pastel2_r">Pastel2 reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
183 <option value="spring_r">spring reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
184 <option value="summer_r">summer reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
185 <option value="autumn_r">autumn reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
186 <option value="winter_r">winter reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
187 <option value="hot_r">hot reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
188 <option value="coolwarm_r">coolwarm reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
189 <option value="cool_r">cool reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
190 <option value="seismic_r">seismic reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
191 <option value="terrain_r">terrain reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
192 <option value="ocean_r">ocean reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
193 <option value="rainbow_r">rainbow reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
194 <option value="bone_r">bone reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
195 <option value="flag_r">flag reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
196 <option value="prism_r">prism reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
197 <option value="cubehelix_r">cubehelix reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
198 <option value="binary_r">binary reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
199 <option value="pink_r">pink reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
200 <option value="gray_r">gray reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
201 <option value="copper_r">copper reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
202 <option value="BrBG_r">BrBG reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
203 <option value="BuGn_r">BuGn reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
204 <option value="BuPu_r">BuPu reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
205 <option value="GnBu_r">GnBu reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
206 <option value="OrRd_r">OrRd reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
207 <option value="PiYG_r">PiYG reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
208 <option value="PRGn_r">PRGn reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
209 <option value="PuOr_r">PuOr reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
210 <option value="PuRd_r">PuRd reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
211 <option value="PuBu_r">PuBu reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
212 <option value="RdBu_r">RdBu reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
213 <option value="RdGy_r">RdGy reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
214 <option value="RdPu_r">RdPu reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
215 <option value="YlGn_r">YlGn reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
216 <option value="PuBuGn_r">PuBuGn reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
217 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
218 <option value="RdYlGn_r">RdYlGn reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
219 <option value="YlGnBu_r">YlGnBu reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
220 <option value="YlOrBr_r">YlOrBr reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
221 <option value="YlOrRd_r">YlOrRd reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
222 <option value="gist_gray_r">gist_gray reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
223 <option value="gist_stern_r">gist_stern reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
224 <option value="gist_earth_r">gist_earth reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
225 <option value="gist_yarg_r">gist_yarg reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
226 <option value="gist_ncar_r">gist_ncar reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
227 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
228 <option value="gist_heat_r">gist_heat reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
229 <option value="gnuplot_r">gnuplot reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
230 <option value="gnuplot2_r">gnuplot2 reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
231 <option value="CMRmap_r">CMRmap reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
232 <option value="bwr_r">bwr reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
233 <option value="hsv_r">hsv reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
234 <option value="brg_r">brg reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
235 <option value="jet_r">jet reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
236 <option value="afmhot_r">afmhot reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
bgruening
parents:
diff
changeset
|
237 <option value="plasma_r">plasma reversed</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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238 </param> |
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239 </xml> |
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240 |
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241 <xml name="multiple_input_matrices"> |
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242 <repeat name="input_files" title="Hi-C Matrix files" min="2"> |
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243 <param name="matrix" type="data" format="h5,cool" label="Hi-C Matrix file" help="" /> |
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244 <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." /> |
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245 </repeat> |
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246 </xml> |
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247 |
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248 <token name="@multiple_input_matrices@"> |
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249 #set $matrices = [] |
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250 #set $mlabels = [] |
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251 #for $counter, $i in enumerate($input_files): |
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252 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; |
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253 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext)) |
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254 |
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255 #if str($i.mlabel.value) != "": |
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256 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)] |
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257 #else |
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258 #set $mlabels += ['\'%s\'' % ($i.matrix.name)] |
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259 #end if |
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260 #end for |
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261 #set $mlabels = ' '.join($mlabels) |
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262 #set $matrices = ' '.join($matrices) |
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263 </token> |
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264 |
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265 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token> |
6b9b4fd51308
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266 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token> |
6b9b4fd51308
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267 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token> |
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268 |
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269 <xml name="region"> |
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270 <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"> |
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271 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator> |
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272 </param> |
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273 </xml> |
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274 |
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275 <xml name="kmeans_clustering"> |
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276 <conditional name="used_multiple_regions"> |
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277 <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."> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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278 <option value="yes">Yes, I used multiple groups of regions</option> |
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279 <option value="no">No, I used only one group</option> |
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280 </param> |
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281 <when value="no"> |
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282 <conditional name="clustering"> |
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283 <param name="clustering_options" type="select" label="Clustering algorithm"> |
6b9b4fd51308
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284 <option value="none">No clustering</option> |
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285 <option value="kmeans">Kmeans clustering</option> |
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286 </param> |
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287 <when value="kmeans"> |
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288 <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)." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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289 </when> |
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290 <when value="none" /> |
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291 </conditional> |
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292 </when> |
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293 <when value="yes" /> |
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294 </conditional> |
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295 </xml> |
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296 |
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297 <token name="@KMEANS_CLUSTERING@"> |
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298 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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299 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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300 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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301 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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302 #end if |
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303 #end if |
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304 #end if |
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305 </token> |
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306 |
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307 <xml name="samFlag"> |
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308 <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)" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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309 </xml> |
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310 <xml name="plotNumbers"> |
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311 <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)" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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312 </xml> |
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313 <xml name="doNotExtendPairedEnds"> |
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314 <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)" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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315 </xml> |
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316 <xml name="ignoreDuplicates"> |
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317 <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)" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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318 </xml> |
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319 <xml name="minMappingQuality"> |
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320 <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. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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321 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. |
6b9b4fd51308
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322 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." /> |
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323 </xml> |
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324 |
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325 <xml name="skipZeros"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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326 <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)" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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327 </xml> |
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328 |
6b9b4fd51308
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329 <xml name="fragmentLength"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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330 <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)" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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331 </xml> |
6b9b4fd51308
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332 |
6b9b4fd51308
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333 <xml name="scaleFactor"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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334 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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335 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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336 </xml> |
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337 <xml name="xMax"> |
1
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338 <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" /> |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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339 </xml> |
6b9b4fd51308
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340 <xml name="filterThreshold"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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341 <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." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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342 <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." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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343 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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344 <xml name="pseudocount"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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345 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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346 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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347 <xml name='matrix_h5_cooler_macro'> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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348 <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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349 </xml> |
6b9b4fd51308
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350 <xml name='matrix_h5_cooler_multiple_macro'> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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351 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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352 </xml> |
2
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353 |
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354 <xml name='matrix_cooler_multiple_macro'> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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355 <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" /> |
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356 </xml> |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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357 <xml name='convertFormat_single_macro'> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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358 <conditional name="inputFormat_conditional"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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359 <param name="inputFormat_selector" type="select" label="Choose input file type"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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360 <option value="optionCool" selected="True">cool</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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361 <option value="optionH5">h5</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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362 <option value="optionHic">hic</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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363 <option value="optionHomer">Homer</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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364 <option value="optionHicpro">HiCPro</option> |
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365 <option value="option2Dtext">2D-text</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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366 |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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367 </param> |
6b9b4fd51308
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368 <when value="optionCool"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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369 <expand macro='matrix_h5_cooler_macro' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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370 <param name='correctionName' type='text' label='Correction factors column name' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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372 <param name='chromosome' type='text' label='Load only one chromosome' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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374 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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375 <when value="optionH5"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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376 <expand macro='matrix_h5_cooler_macro' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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377 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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378 <when value="optionHic"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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379 <param name='matrixHic' type='data' format='hic' label='.hic matrix' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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380 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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381 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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382 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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383 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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384 <when value="optionHomer"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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386 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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387 <when value="optionHicpro"> |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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388 <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' /> |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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389 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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390 </when> |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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391 <when value="option2Dtext"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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392 <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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393 |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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394 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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395 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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396 </param> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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397 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' /> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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398 </when> |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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399 </conditional> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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400 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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401 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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402 <xml name='convertFormat_multiple_macro'> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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403 <conditional name="inputFormat_conditional"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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404 <param name="inputFormat_selector" type="select" label="Choose input file type"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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405 <option value="optionCool" selected="True">cool</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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406 <option value="optionH5">h5</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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407 <option value="optionHomer">Homer</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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408 <option value="optionHicpro">HiCPro</option> |
2
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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409 <option value="option2Dtext">2D-text</option> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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410 |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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411 |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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412 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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413 <when value="optionCool"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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414 <expand macro='matrix_h5_cooler_multiple_macro' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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415 <param name='correctionName' type='text' label='Correction factors column name' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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416 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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417 <param name='chromosome' type='text' label='Load only one chromosome' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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418 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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419 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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420 <when value="optionH5"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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421 <expand macro='matrix_h5_cooler_multiple_macro' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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422 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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423 <when value="optionHomer"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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424 <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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425 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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426 <when value="optionHicpro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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427 <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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428 <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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429 </when> |
2
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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430 <when value="option2Dtext"> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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431 <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' /> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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432 |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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433 <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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1
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434 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
1
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|
435 </param> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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436 <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' /> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
1
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|
437 </when> |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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438 </conditional> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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439 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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440 <xml name='convertFormat_single_output_macro'> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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441 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> --> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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442 <conditional name="outputFormat_conditional"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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443 <param name="outputFormat_selector" type="select" label="Choose output file type"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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444 <option value="cool" selected="True">cool</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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445 <option value="h5">h5</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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446 <option value="homer">Homer</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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447 <option value="ginteractions">ginteractions</option> |
2
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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448 <option value="hicpro">hicpro</option> |
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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449 |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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450 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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451 <when value="cool"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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452 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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453 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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454 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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455 <when value='h5' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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456 <when value='homer' /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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457 <when value='ginteractions' /> |
2
b376ef118807
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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|
458 <when value='hicpro' /> |
0
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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459 </conditional> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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460 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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461 <token name="@REFERENCES@"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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462 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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463 .. class:: infomark |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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464 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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465 For more information on the tools, please visit our `help site`_. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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466 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
467 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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468 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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469 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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470 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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471 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
472 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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473 .. _help site: https://hicexplorer.readthedocs.org |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
474 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
475 </token> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
476 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
477 <xml name="multiple_input_bams"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
478 <repeat name="input_files" title="BAM files" min="2"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
479 <param name="bamfile" type="data" format="bam" label="BAM file" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
480 <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." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
481 </repeat> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
482 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
483 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
484 <xml name="multiple_input_bigwigs"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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diff
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|
485 <repeat name="input_files" title="BigWig files" min="2"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
486 <param name="bigwigfile" type="data" format="bigwig" label="Bigwig file" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
487 <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."> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
488 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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489 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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490 </repeat> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
491 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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492 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
493 <xml name="plotTitle"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
494 <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)"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
495 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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496 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
497 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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498 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
499 <token name="@multiple_input_bams@"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
500 #import tempfile |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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501 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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502 #set files=[] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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503 #set labels=[] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
504 #for $i in $input_files: |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
505 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
506 #set $temp_input_path = $temp_input_handle.name |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
507 #silent $temp_input_handle.close() |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
508 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
509 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
510 #silent $files.append('%s.bam' % $temp_input_path) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
511 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
512 ##set $files += [str($i.bamfile)] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
513 #if str($i.label.value) != "": |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
514 #set $labels += ["\"%s\"" % ($i.label.value)] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
515 #else |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
516 #set $labels += ["\"%s\"" % ($i.bamfile.name)] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
517 #end if |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
518 #end for |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
519 </token> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
520 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
521 <token name="@multiple_input_bigwigs@"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
522 #import tempfile |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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parents:
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|
523 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
524 #set files=[] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
525 #set labels=[] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
526 #for $i in $input_files: |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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parents:
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|
527 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
528 #set $temp_input_path = $temp_input_handle.name |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
529 #silent $temp_input_handle.close() |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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parents:
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changeset
|
530 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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parents:
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changeset
|
531 #silent $files.append('%s.bw' % $temp_input_path) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
532 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
533 ##set $files += [str($i.bigwigfile)] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
534 #if str($i.label.value) != "": |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
535 #set $labels += ["\"%s\"" % ($i.label.value)] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
536 #else |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
537 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
538 #end if |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
539 #end for |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
540 </token> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
541 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
542 <xml name="reference_genome_source"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
543 <conditional name="source"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
544 <param name="ref_source" type="select" label="Reference genome"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
545 <option value="cached">locally cached</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
546 <option value="history">in your history</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
547 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
548 <when value="cached"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
549 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
550 <options from_data_table="deepTools_seqs"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
551 <filter type="sort_by" column="1" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
552 <validator type="no_options" message="No indexes are available." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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553 </options> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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554 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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555 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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556 <when value="history"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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557 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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558 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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559 </conditional> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
560 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
561 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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562 <token name="@reference_genome_source@"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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563 #if $source.ref_source=="history": |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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564 --genome $source.input1 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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565 #else: |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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566 --genome "${source.input1_2bit.fields.path}" |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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567 #end if |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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568 </token> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
569 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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570 <xml name="effectiveGenomeSize"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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571 <conditional name="effectiveGenomeSize"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
572 <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. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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573 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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574 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."> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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575 <option value="93260000">ce10 (93260000)</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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576 <option value="121400000">dm3 (121400000)</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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577 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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578 <option value="2150570000">mm9 (2150570000)</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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579 <option value="specific">user specified</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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580 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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581 <when value="specific"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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582 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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583 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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584 <when value="2150570000" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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585 <when value="2451960000" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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586 <when value="121400000" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
587 <when value="93260000" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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588 </conditional> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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589 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
590 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
591 <xml name="image_file_format"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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592 <param name="outFileFormat" type="select" label="Image file format"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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593 <option value="png" selected="true">png</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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594 <option value="pdf">pdf</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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595 <option value="svg">svg</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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596 <option value="eps">eps</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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597 <option value="emf">emf</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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598 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
599 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
600 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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601 <xml name="missingDataAsZero"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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602 <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." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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603 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
604 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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605 <xml name="input_save_matrix_values"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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606 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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607 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
608 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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609 <xml name="input_graphic_output_settings"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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610 <conditional name="output"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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611 <param name="showOutputSettings" type="select" label="Show advanced output settings"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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612 <option value="no" selected="true">no</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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613 <option value="yes">yes</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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614 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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615 <when value="no" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
616 <when value="yes"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
617 <yield /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
618 <param name="saveData" type="boolean" label="Save the data underlying the average profile" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
619 <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." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
620 </when> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
621 </conditional> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
622 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
623 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
624 <xml name="input_image_file_format"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
625 <param name="outFileFormat" type="select" label="Image file format"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
626 <option value="png" selected="true">png</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
627 <option value="pdf">pdf</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
628 <option value="svg">svg</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
629 <option value="eps">eps</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
630 <option value="emf">emf</option> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
631 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
632 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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changeset
|
633 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
634 <xml name="output_image_file_format"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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635 <data format="png" name="outFileName" label="${tool.name} image"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
636 <change_format> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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637 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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638 <when input="output.outFileFormat" value="svg" format="svg" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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639 <when input="output.outFileFormat" value="eps" format="eps" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
640 <when input="output.outFileFormat" value="emf" format="emf" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
641 </change_format> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
642 </data> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
643 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
644 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
645 <xml name="output_save_matrix_values"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
646 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
647 <filter> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
648 (( |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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649 output['showOutputSettings'] == 'yes' and |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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650 output['saveMatrix'] is True |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
651 )) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
652 </filter> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
653 </data> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
654 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
655 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
656 <xml name="output_graphic_outputs"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
657 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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658 <filter> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
659 (( |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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660 output['showOutputSettings'] == 'yes' and |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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661 output['saveData'] is True |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
662 )) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
663 </filter> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
664 </data> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
665 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
666 <filter> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
667 (( |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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668 output['showOutputSettings'] == 'yes' and |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
669 output['saveSortedRegions'] is True |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
670 )) |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
671 </filter> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
672 </data> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
673 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
674 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
675 <xml name="track_input_h5_macro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
676 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
677 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
678 <xml name="track_input_bed_macro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
679 <param name="track_input_bed" type="data" format="bed" label="Track file BED format" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
680 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
681 <xml name="track_input_bedgraph_macro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
682 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
683 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
684 <xml name="track_input_bigwig_macro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
685 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
686 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
687 <xml name="track_input_bedgraph_matrix_macro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
688 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
689 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
690 <xml name="track_input_tabular_macro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
691 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
692 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
693 <xml name="plot_title"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
694 <param name="title" type="text" optional="true" label="Plot title"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
695 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
696 </param> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
697 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
698 |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
699 <xml name="spacer_macro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
700 <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." /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
701 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
702 <xml name="fontsize_macro"> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
703 <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" /> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
704 </xml> |
6b9b4fd51308
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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|
705 </macros> |