Mercurial > repos > bgruening > hicexplorer_chicviewpointbackgroundmodel

comparison chicViewpointBackgroundModel.xml @ 2:b9cdce1e57a1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 17:18:30 -0400
parents 91abc3b2e948
children 7fe1a401d833
comparison
equal deleted inserted replaced
1:91abc3b2e948 2:b9cdce1e57a1
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>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 9
10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple): 10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
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 16
17 --matrices $m 17 --matrices $m
18 --averageContactBin $averageContactBin 18 --averageContactBin $averageContactBin
19 --fixateRange $fixateRange 19 --fixateRange $fixateRange
21 --threads @THREADS@ 21 --threads @THREADS@
22 --outFileName background.txt 22 --outFileName background.txt
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <expand macro="matrix_h5_cooler_multiple_macro" /> 25 <expand macro="matrix_h5_cooler_multiple_macro" />
26 26
27 <param argument="--referencePoints" type="data" format='interval' 27 <param argument="--referencePoints" type="data" format='interval'
28 label="Reference points" 28 label="Reference points"
29 help="Bed file contains all reference points which should be used to build the background model." /> 29 help="Bed file contains all reference points which should be used to build the background model." />
30 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/> 30 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
31 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/> 31 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
32 32
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/> 35 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/>
36 </outputs> 36 </outputs>
37 <tests> 37 <tests>
38 <test> 38 <test>
39 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 39 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
40 40
41 <param name="referencePoints" value="cHi-C/referencePoints.bed"/> 41 <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
42 42
43 <output name="background" file="cHi-C/background.bed" ftype="tabular" compare="sim_size" delta='40000'/> 43 <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/>
44 </test> 44 </test>
45 </tests> 45 </tests>
46 <help><![CDATA[ 46 <help><![CDATA[
47 47
48 Compute a background model for cHi-C data analysis 48 Compute a background model for cHi-C data analysis