Mercurial > repos > bgruening > hicexplorer_chicviewpointbackgroundmodel

comparison chicViewpointBackgroundModel.xml @ 6:628259b7ffb4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:17:34 +0000
parents 7fe1a401d833
children 9d02f1819e81
comparison
equal deleted inserted replaced
5:83570b36593e 6:628259b7ffb4
1 <tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>compute a background model for cHi-C / HiChIP data</description> 2 <description>compute a background model for cHi-C / HiChIP data</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicViewpointBackgroundModel</token> 4 <token name="@BINARY@">chicViewpointBackgroundModel</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
11 ln -s '$m' '${counter}_matrix.$m.ext' && 11 ln -s '$m' '${counter}_matrix.$m.ext' &&
12 #end for 12 #end for
13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) 13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
14 14
15 @BINARY@ 15 @BINARY@
16
17 --matrices $m 16 --matrices $m
18 --averageContactBin $averageContactBin 17 --averageContactBin $averageContactBin
19 --fixateRange $fixateRange 18 --fixateRange $fixateRange
20 --referencePoints '$referencePoints' 19 --referencePoints '$referencePoints'
21 $truncateZeros 20 $truncateZeros
22 --threads @THREADS@ 21 --threads @THREADS@
23 --outFileName background.txt 22 --outFileName background.txt
24 ]]></command> 23 ]]> </command>
25 <inputs> 24 <inputs>
26 <expand macro="matrix_h5_cooler_multiple_macro" /> 25 <expand macro="matrix_h5_cooler_multiple_macro" />
27 26 <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to build the background model." />
28 <param argument="--referencePoints" type="data" format='interval' 27 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.' />
29 label="Reference points" 28 <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.' />
30 help="Bed file contains all reference points which should be used to build the background model." /> 29 <param argument='--truncateZeros' type='boolean' truevalue='--truncateZeros' falsevalue="" checked="false" label="Truncate zeros" help="Set this parameter if you want truncate zeros to fight over dispersion." />
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.'/>
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.'/>
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."/>
35 </inputs> 30 </inputs>
36 <outputs> 31 <outputs>
37 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/> 32 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model" />
38 </outputs> 33 </outputs>
39 <tests> 34 <tests>
40 <test> 35 <test expect_num_outputs="1">
41 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 36 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
42 <param name="referencePoints" value="cHi-C/referencePoints.bed"/> 37 <param name="referencePoints" value="cHi-C/referencePoints.bed" />
43 <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/> 38 <output name="background" ftype="tabular">
39 <assert_contents>
40 <has_text text="-500000" />
41 <has_text text="-498000" />
42 <has_n_columns n="5" />
43 <has_text text="nbinom" />
44 </assert_contents>
45 </output>
44 </test> 46 </test>
45 <test> 47 <test expect_num_outputs="1">
46 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 48 <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"/> 49 <param name="truncateZeros" value="True" />
48 <param name="referencePoints" value="cHi-C/referencePoints.bed"/> 50 <param name="referencePoints" value="cHi-C/referencePoints.bed" />
49 <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/> 51 <output name="background" ftype="tabular">
52 <assert_contents>
53 <has_text text="476000" />
54 <has_text text="491000" />
55 <has_n_columns n="5" />
56 <has_text text="nbinom" />
57 </assert_contents>
58 </output>
50 </test> 59 </test>
51 </tests> 60 </tests>
52 <help><![CDATA[ 61 <help><![CDATA[
53 62
54 Compute a background model for cHi-C data analysis 63 Compute a background model for cHi-C data analysis
61 The background distributions are fixed at `--fixateRange` i.e. all distances lower / higher than this value use the fixed background distribution. 70 The background distributions are fixed at `--fixateRange` i.e. all distances lower / higher than this value use the fixed background distribution.
62 71
63 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 72 For more information about HiCExplorer please consider our documentation on readthedocs.io_
64 73
65 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 74 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
66 ]]></help> 75 ]]> </help>
67 <expand macro="citations" /> 76 <expand macro="citations" />
68 </tool> 77 </tool>