Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts
comparison hicPlotDistVsCounts.xml @ 5:819bd2c44d4a draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author | bgruening |
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date | Sat, 30 Dec 2017 09:29:00 -0500 |
parents | ed96f2fd7e3f |
children | 62803bb47880 |
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4:ed96f2fd7e3f | 5:819bd2c44d4a |
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9 #import re | 9 #import re |
10 #set matrices_path=[] | 10 #set matrices_path=[] |
11 #set matrices_labels=[] | 11 #set matrices_labels=[] |
12 #for $counter, $m, in enumerate($matrices): | 12 #for $counter, $m, in enumerate($matrices): |
13 #set identifier = re.sub('[^\s\w\-]', '_', str($m.element_identifier)) | 13 #set identifier = re.sub('[^\s\w\-]', '_', str($m.element_identifier)) |
14 ln -f -s '${m}' '${identifier}_${counter}.npz.h5' && | 14 ln -f -s '${m}' '${identifier}_${counter}' && |
15 #silent $matrices_path.append("'%s_%s.npz.h5'" % ($identifier, $counter)) | 15 #silent $matrices_path.append("'%s_%s'" % ($identifier, $counter)) |
16 #silent $matrices_labels.append("'%s'" % ($identifier)) | 16 #silent $matrices_labels.append("'%s'" % ($identifier)) |
17 #end for | 17 #end for |
18 | 18 |
19 @BINARY@ | 19 @BINARY@ |
20 --matrices #echo " ".join($matrices_path)# | 20 --matrices #echo " ".join($matrices_path)# |
31 --chromosomeExclude '$chroms' | 31 --chromosomeExclude '$chroms' |
32 #end if | 32 #end if |
33 ]]> | 33 ]]> |
34 </command> | 34 </command> |
35 <inputs> | 35 <inputs> |
36 <param argument="--matrices" type="data" format="h5" multiple="True" label="HiC normalized (corrected) matrices"/> | 36 <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="HiC normalized (corrected) matrices"/> |
37 | 37 |
38 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" /> | 38 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" /> |
39 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome" | 39 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome" |
40 help="If more than one HiC matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." /> | 40 help="If more than one HiC matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." /> |
41 <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth" | 41 <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth" |