Mercurial > repos > bgruening > hicexplorer_hicmergeloops

comparison hicMergeLoops.xml @ 2:59d3fa4c16f5 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 17:03:53 -0400
parents 49b82255b72f
children 94b552c6830a
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1:aeb4f3e6678d 2:59d3fa4c16f5
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #for $counter, $loopfile in enumerate($inputFiles): 9 #for $counter, $loopfile in enumerate($inputFiles):
10 ln -s '$loopfile' '${counter}_loop_file.bedgraph' && 10 ln -s '$loopfile' '${counter}_loop_file.bedgraph' &&
11 #end for 11 #end for
12 #set $m = ' '.join([ '\'%s_loop_file.bedgraph\'' % $counter for $counter, $inputfile in enumerate($inputFiles) ]) 12 #set $m = ' '.join([ '\'%s_loop_file.bedgraph\'' % $counter for $counter, $inputfile in enumerate($inputFiles) ])
13 13
14 @BINARY@ 14 @BINARY@
15 --inputFiles $m 15 --inputFiles $m
16 --lowestResolution $lowestResolution 16 --lowestResolution $lowestResolution
17 --outFileName merged_loops.bedgraph 17 --outFileName merged_loops.bedgraph
18 ]]></command> 18 ]]></command>
19 <inputs> 19 <inputs>
20 <param argument="--inputFiles" type="data" format='bed' 20 <param argument="--inputFiles" type="data" format='bed'
21 label="Loop files to merge" 21 label="Loop files to merge"
22 help="The loop files from hicDetectLoops. To use files from other sources, 22 help="The loop files from hicDetectLoops. To use files from other sources,
23 please follow \'chr start end chr start end\' format and remove any header." multiple="true" /> 23 please follow \'chr start end chr start end\' format and remove any header." multiple="true" />
24 <param argument="--lowestResolution" type="integer" value="" 24 <param argument="--lowestResolution" type="integer" value=""
25 label="Lowest used resolution" 25 label="Lowest used resolution"
26 help='The lowest resolution of all loop files, i.e. 5kb, 10kb and 25kb, please use 25000.'/> 26 help='The lowest resolution of all loop files, i.e. 5kb, 10kb and 25kb, please use 25000.'/>
27 </inputs> 27 </inputs>
28 <outputs> 28 <outputs>
29 <data name="mergedLoops" from_work_dir="merged_loops.bedgraph" format="bed" label="${tool.name} on [${on_string}]: Merged loops"/> 29 <data name="mergedLoops" from_work_dir="merged_loops.bedgraph" format="bed" label="${tool.name} on [${on_string}]: Merged loops"/>
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>
40 Merge detected loops 40 Merge detected loops
41 ==================== 41 ====================
42 42
43 This script merges the loop locations of different different resolutions. 43 This script merges the loop locations of different different resolutions.
44 44
45 Loops need to have format as follows: 45 Loops need to have the following format:
46 46
47 chr start end chr start end 47 chr start end chr start end
48 48
49 A merge happens if x and y position of a loop overlap with x and y position of another loop; all loops are considered as an overlap within +/- the bin size of the lowest resolution. 49 A merge happens if x and y position of a loop overlaps with x and y position of another loop; all loops are considered as an overlap within +/- the bin size of the lowest resolution.
50 I.e. for a loop with coordinates x and y, the overlap to all other loops is search for (x - lowest resolution) and (y + lowest resolution). 50 I.e. for a loop with coordinates x and y, the overlap to all other loops is searched for (x - lowest resolution) and (y + lowest resolution).
51 If two or more locations should be merged, the one with the lowest resolution is taken as the merged loop. 51 If two or more locations should be merged, the one with the lowest resolution is taken as the merged loop.
52 52
53 Example usage: 53 Example usage:
54 54
55 `$ hicMergeLoops -i gm12878_10kb.bedgraph gm12878_5kb.bedgraph gm12878_25kb.bedgraph -o merged_result.bedgraph -r 25000` 55 `$ hicMergeLoops -i gm12878_10kb.bedgraph gm12878_5kb.bedgraph gm12878_25kb.bedgraph -o merged_result.bedgraph -r 25000`