Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions

comparison chicSignificantInteractions.xml @ 3:7668fac6cc3a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
author iuc
date Tue, 24 Mar 2020 13:42:40 -0400
parents 3df84bb4486c
children 38fa8a72ece6
comparison
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2:3df84bb4486c 3:7668fac6cc3a
47 --resolution $resolution 47 --resolution $resolution
48 --peakInteractionsThreshold $peakInteractionsThreshold 48 --peakInteractionsThreshold $peakInteractionsThreshold
49 --range $rangeUpstream $rangeDownstream 49 --range $rangeUpstream $rangeDownstream
50 --targetFolder targetFolder 50 --targetFolder targetFolder
51 --outputFolder significantFilesFolder 51 --outputFolder significantFilesFolder
52 52 $truncateZeroPvalues
53 --xFoldMaxValueNB $xFoldMaxValueNB
54 --fixateRange $fixateRange 53 --fixateRange $fixateRange
55 -suffix significant_interactions.txt 54 -suffix significant_interactions.txt
56 --threads @THREADS@ 55 --threads @THREADS@
57 ]]></command> 56 ]]></command>
58 <inputs> 57 <inputs>
93 <param argument="--resolution" type="integer" value="1000" label="Bin resolution of the used data" help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution. 92 <param argument="--resolution" type="integer" value="1000" label="Bin resolution of the used data" help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.
94 This value is used to merge neighboring bins.'/> 93 This value is used to merge neighboring bins.'/>
95 <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.' /> 94 <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.' />
96 <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.' /> 95 <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.' />
97 <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.'/> 96 <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.'/>
98 <param argument="--xFoldMaxValueNB" type="integer" value="10" label="x-fold for NB distributions" help='x-fold factor to increase the number of precomputed p-values per relative genomic distance. If set to 1, the maximal distance is used.'/> 97 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one."
98 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."/>
99 </inputs> 99 </inputs>
100 <outputs> 100 <outputs>
101 <collection name="significantFilesCollection" type="list" label="Significant files"> 101 <collection name="significantFilesCollection" type="list" label="Significant files">
102 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" /> 102 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" />
103 </collection> 103 </collection>
129 <param name="backgroundModelFile" value="cHi-C/background.txt"/> 129 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
130 <param name="rangeUpstream" value="200000"/> 130 <param name="rangeUpstream" value="200000"/>
131 <param name="rangeDownstream" value="200000"/> 131 <param name="rangeDownstream" value="200000"/>
132 132
133 <output_collection name="significantFilesCollection" type="list" count="6"> 133 <output_collection name="significantFilesCollection" type="list" count="6">
134 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt" ftype="interval" lines_diff="4"/> 134 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/>
135 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4"/> 135 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4"/>
136 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt" ftype="interval" lines_diff="4"/> 136 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4"/>
137 137
138 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt" ftype="interval" lines_diff="4"/> 138 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/>
139 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4"/> 139 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4"/>
140 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt" ftype="interval" lines_diff="4"/> 140 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4"/>
141 </output_collection> 141 </output_collection>
142 142
143 <output_collection name="targetFilesCollection" type="list" count="3"> 143 <output_collection name="targetFilesCollection" type="list" count="3">
144 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval" lines_diff="4"/> 144 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval" lines_diff="4"/>
145 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/> 145 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/>