Mercurial > repos > bgruening > hicexplorer_chicviewpointbackgroundmodel

comparison chicViewpointBackgroundModel.xml @ 3:7fe1a401d833 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 14:22:19 -0400
parents b9cdce1e57a1
children 628259b7ffb4
comparison
equal deleted inserted replaced
2:b9cdce1e57a1 3:7fe1a401d833
16 16
17 --matrices $m 17 --matrices $m
18 --averageContactBin $averageContactBin 18 --averageContactBin $averageContactBin
19 --fixateRange $fixateRange 19 --fixateRange $fixateRange
20 --referencePoints '$referencePoints' 20 --referencePoints '$referencePoints'
21 $truncateZeros
21 --threads @THREADS@ 22 --threads @THREADS@
22 --outFileName background.txt 23 --outFileName background.txt
23 ]]></command> 24 ]]></command>
24 <inputs> 25 <inputs>
25 <expand macro="matrix_h5_cooler_multiple_macro" /> 26 <expand macro="matrix_h5_cooler_multiple_macro" />
27 <param argument="--referencePoints" type="data" format='interval' 28 <param argument="--referencePoints" type="data" format='interval'
28 label="Reference points" 29 label="Reference points"
29 help="Bed file contains all reference points which should be used to build the background model." /> 30 help="Bed file contains all reference points which should be used to build the background model." />
30 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/> 31 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
31 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/> 32 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
32 33 <param name='truncateZeros' type='boolean' truevalue='--truncateZeros' falsevalue="" checked="false" label="Truncate zeros"
34 help="Set this parameter if you want truncate zeros to fight over dispersion."/>
33 </inputs> 35 </inputs>
34 <outputs> 36 <outputs>
35 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/> 37 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/>
36 </outputs> 38 </outputs>
37 <tests> 39 <tests>
38 <test> 40 <test>
39 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 41 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
40
41 <param name="referencePoints" value="cHi-C/referencePoints.bed"/> 42 <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
42 43 <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/>
44 </test>
45 <test>
46 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
47 <param name="truncateZeros" value="True"/>
48 <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
43 <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/> 49 <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/>
44 </test> 50 </test>
45 </tests> 51 </tests>
46 <help><![CDATA[ 52 <help><![CDATA[
47 53