Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions
annotate chicSignificantInteractions.xml @ 10:f8320df1866b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
author | iuc |
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date | Tue, 05 Nov 2024 00:06:29 +0000 |
parents | 640e0e45518a |
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6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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1 <tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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2 <description>computes viewpoints with the given reference points and a background model</description> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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3 <macros> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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4 <token name="@BINARY@">chicSignificantInteractions</token> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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5 <import>macros.xml</import> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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6 </macros> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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7 <expand macro="requirements" /> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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8 <command detect_errors="exit_code"><![CDATA[ |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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9 #import re |
8
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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10 |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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11 @BINARY@ |
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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12 |
8
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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13 --interactionFile '$interactionFile' |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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14 |
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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15 --pValue $pvalue |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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16 |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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17 #if $filter_conditional.filter_selector == 'optionXfold': |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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18 --xFoldBackground $filter_conditional.xfold |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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19 #else: |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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20 --loosePValue $filter_conditional.loosePvalue |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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21 |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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22 #end if |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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23 --backgroundModelFile '$backgroundModelFile' |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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24 --peakInteractionsThreshold $peakInteractionsThreshold |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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25 --range $rangeUpstream $rangeDownstream |
8
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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26 --combinationMode $mode_selector |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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27 --outFileNameSignificant significant.hdf5 |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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28 --outFileNameTarget target.hdf5 |
3
7668fac6cc3a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
iuc
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29 $truncateZeroPvalues |
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2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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30 --fixateRange $fixateRange |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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31 --threads @THREADS@ |
4
38fa8a72ece6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
iuc
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32 |
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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33 ]]> </command> |
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2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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34 <inputs> |
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640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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35 <param name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" /> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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36 |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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37 <param name="pvalue" type="float" value="0.05" label="P-value of interaction to be accepted as significant" /> |
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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38 <conditional name="filter_conditional"> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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39 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions"> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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40 <option value="optionXfold">x-fold over mean background</option> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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41 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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42 </param> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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43 <when value="optionXfold"> |
8
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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44 <param name="xfold" type="float" value="2.0" label="X-fold over mean background to be accepted." help="Filter x-fold over background. |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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45 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. Used only for pValue option." /> |
0
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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46 </when> |
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3df84bb4486c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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47 <when value="optionLoosePvalue"> |
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640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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48 <param name="loosePvalue" type="float" value="0.3" label="Loose p-value" help="loose p-value threshold value to filter target regions in a first round. |
6
6001400eed99
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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49 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. |
8
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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50 Used only for pValue option." /> |
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2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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51 </when> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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52 </conditional> |
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640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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53 |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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54 <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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55 <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help="The minimum number of interactions a detected peaks needs to have to be considered." /> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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56 |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
parents:
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57 <param name="mode_selector" type="select" label="Process matrices independently or combine always two (for differential analysis preparation)"> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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58 <option value="dual">Dual</option> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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59 <option value="single" selected="True">Single</option> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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60 </param> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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61 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." /> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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62 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." /> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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63 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help="Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin." /> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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64 <param name="truncateZeroPvalues" type="boolean" truevalue="--truncateZeroPvalues" falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." /> |
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2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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65 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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66 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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67 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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68 <data name="significantFile" from_work_dir="significant.hdf5" format="h5" label="${tool.name} significant file" /> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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69 <data name="targetFile" from_work_dir="target.hdf5" format="h5" label="${tool.name} target file" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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70 </outputs> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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71 <tests> |
2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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72 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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73 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> |
640e0e45518a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
iuc
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74 <param name="pvalue" value="0.2" /> |
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2f279a01f3ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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75 |
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76 <conditional name="filter_conditional"> |
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77 <param name="filter_selector" value="optionLoosePvalue" /> |
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78 <param name="loosePvalue" value="0.5" /> |
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79 </conditional> |
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80 <param name="mode_selector" value="dual" /> |
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81 <param name="backgroundModelFile" value="cHi-C/background.txt" /> |
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82 <param name="rangeUpstream" value="200000" /> |
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83 <param name="rangeDownstream" value="200000" /> |
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84 |
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85 <output name="significantFile" ftype="h5"> |
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86 <assert_contents> |
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87 <has_h5_attribute key="combinationMode" value="dual" /> |
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88 <has_h5_attribute key="mode_preselection" value="loosePValue" /> |
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89 <has_h5_attribute key="type" value="significant" /> |
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90 </assert_contents> |
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91 </output> |
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92 |
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93 <output name="targetFile" ftype="h5"> |
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94 <assert_contents> |
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95 <has_h5_attribute key="combinationMode" value="dual" /> |
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96 <has_h5_attribute key="mode_preselection" value="loosePValue" /> |
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97 <has_h5_attribute key="type" value="target" /> |
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98 </assert_contents> |
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99 </output> |
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100 </test> |
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101 |
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102 </tests> |
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103 <help><![CDATA[ |
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104 |
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105 Significant interaction detection |
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106 ================================= |
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107 |
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108 Significant interactions are detected by this tool for each viewpoint based on the background model. chicSignificantInteractions outputs for each viewpoint a file containing all recorded significant interactions and |
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109 a target file. The target file is especially useful in the batch mode context, as it merges for two consecutive listed control and treatment viewpoint the significant interactions which can then be used |
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110 to test for a differential interaction scheme. |
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111 |
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112 chicSignificantInteractions supports two modes to detect significant interactions, either by an x-fold over the average background or a loose p-value. In both cases neighboring significant peaks are merged together and an additional |
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113 p-value based on the sum of interactions for this neighborhood is computed. Only interactions with a higher p-value as specified by the threshold `--pValue` are accepted as a significant interaction. |
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114 |
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115 For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
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116 |
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117 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
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118 ]]> </help> |
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119 <expand macro="citations" /> |
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120 </tool> |