Mercurial > repos > bgruening > deeptools_plot_enrichment

comparison plotEnrichment.xml @ 6:f3580352b9d8 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
author bgruening
date Fri, 31 Mar 2017 08:11:51 -0400
parents c53dcf458fc0
children f8b1d1ae388e
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equal deleted inserted replaced
5:50efa005c0c6 6:f3580352b9d8
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10
11 @multiple_input_bams@ 10 @multiple_input_bams@
12 @BINARY@ 11 @BINARY@
13 @THREADS@ 12 @THREADS@
14 13
15 --plotFile '$outFileName' 14 --plotFile '$outFileName'
61 --numPlotsPerRow '$advancedOpt.numPlotsPerRow' 60 --numPlotsPerRow '$advancedOpt.numPlotsPerRow'
62 61
63 --alpha '$advancedOpt.alpha' 62 --alpha '$advancedOpt.alpha'
64 63
65 @ADVANCED_OPTS_READ_PROCESSING@ 64 @ADVANCED_OPTS_READ_PROCESSING@
65
66 #if $advancedOpt.Offset:
67 --Offset $advancedOpt.Offset
68 #end if
66 69
67 @blacklist@ 70 @blacklist@
68 71
69 $advancedOpt.keepExons 72 $advancedOpt.keepExons
70 73
131 <expand macro="read_processing_options" /> 134 <expand macro="read_processing_options" />
132 135
133 <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue="" 136 <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
134 label="Include BED12 exons" 137 label="Include BED12 exons"
135 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." /> 138 help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />
139
140 <param argument="--Offset" type="text" value="" optional="True"
141 label="Offset inside each alignment to use for the signal location."
142 help="Uses this offset inside of each read as the signal. This is useful in
143 cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
144 should be used to denote where the signal is (rather than the span of the
145 whole alignment). This can be paired with the --filterRNAstrand option. Note
146 that negative values indicate offsets from the end of each read. A value of
147 1 indicates the first base of the alignment (taking alignment orientation
148 into account). Likewise, a value of -1 is the last base of the alignment. An
149 offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
150 used to specify a range of positions. Note that specifying something like
151 --Offset 5 -1 will result in the 5th through last position being used, which
152 is equivalent to trimming 4 bases from the 5-prime end of alignments." />
136 153
137 <expand macro="blacklist" /> 154 <expand macro="blacklist" />
138 155
139 </expand> 156 </expand>
140 157