Mercurial > repos > bgruening > hicexplorer_hicmergeloops

comparison hicMergeLoops.xml @ 0:49b82255b72f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:30:48 -0500
parents
children 59d3fa4c16f5
comparison
equal deleted inserted replaced
-1:000000000000 0:49b82255b72f
1 <tool id="hicexplorer_hicmergeloops" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>merge detected loops of different resolutions.</description>
3 <macros>
4 <token name="@BINARY@">hicMergeLoops</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 #for $counter, $loopfile in enumerate($inputFiles):
10 ln -s '$loopfile' '${counter}_loop_file.bedgraph' &&
11 #end for
12 #set $m = ' '.join([ '\'%s_loop_file.bedgraph\'' % $counter for $counter, $inputfile in enumerate($inputFiles) ])
13
14 @BINARY@
15 --inputFiles $m
16 --lowestResolution $lowestResolution
17 --outFileName merged_loops.bedgraph
18 ]]></command>
19 <inputs>
20 <param argument="--inputFiles" type="data" format='bed'
21 label="Loop files to merge"
22 help="The loop files from hicDetectLoops. To use files from other sources,
23 please follow \'chr start end chr start end\' format and remove any header." multiple="true" />
24 <param argument="--lowestResolution" type="integer" value=""
25 label="Lowest used resolution"
26 help='The lowest resolution of all loop files, i.e. 5kb, 10kb and 25kb, please use 25000.'/>
27 </inputs>
28 <outputs>
29 <data name="mergedLoops" from_work_dir="merged_loops.bedgraph" format="bed" label="${tool.name} on [${on_string}]: Merged loops"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="inputFiles" ftype='bed' value="hicMergeLoops/gm12878_10kb.bedgraph,hicMergeLoops/gm12878_5kb.bedgraph,hicMergeLoops/gm12878_25kb.bedgraph"/>
34 <param name="lowestResolution" value="25000"/>
35 <output name="mergedLoops" file="hicMergeLoops/gm12878_all.bedgraph" ftype="bed" compare="sim_size" delta='40000'/>
36 </test>
37 </tests>
38 <help><![CDATA[
39
40 Merge detected loops
41 ====================
42
43 This script merges the loop locations of different different resolutions.
44
45 Loops need to have format as follows:
46
47 chr start end chr start end
48
49 A merge happens if x and y position of a loop overlap with x and y position of another loop; all loops are considered as an overlap within +/- the bin size of the lowest resolution.
50 I.e. for a loop with coordinates x and y, the overlap to all other loops is search for (x - lowest resolution) and (y + lowest resolution).
51 If two or more locations should be merged, the one with the lowest resolution is taken as the merged loop.
52
53 Example usage:
54
55 `$ hicMergeLoops -i gm12878_10kb.bedgraph gm12878_5kb.bedgraph gm12878_25kb.bedgraph -o merged_result.bedgraph -r 25000`
56
57 Please recall: We work with binned data i.e. the lowest resolution is therefore the one where we merge the most bases into one bin. In the above example the lowest resultion is 25kb, the highest resolution is 5kb.
58
59
60 For more information about HiCExplorer please consider our documentation on readthedocs.io_
61
62 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
63 ]]></help>
64 <expand macro="citations" />
65 </tool>