Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

comparison hicPlotDistVsCounts.xml @ 5:819bd2c44d4a draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:29:00 -0500
parents ed96f2fd7e3f
children 62803bb47880
comparison
equal deleted inserted replaced
4:ed96f2fd7e3f 5:819bd2c44d4a
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"