Mercurial > repos > bgruening > deeptools_bam_coverage

comparison bamCoverage.xml @ 12:22bfbb186bf1 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 08:08:52 -0400
parents aa33302db115
children f024daeffbed
comparison
equal deleted inserted replaced
11:41b3f35b7563 12:22bfbb186bf1
19 19
20 --binSize $binSize 20 --binSize $binSize
21 21
22 #if $scaling.type=='rpkm': 22 #if $scaling.type=='rpkm':
23 --normalizeUsingRPKM 23 --normalizeUsingRPKM
24 --scaleFactor $scaling.scaleFactor
25 #elif $scaling.type=='1x': 24 #elif $scaling.type=='1x':
26 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": 25 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
27 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize 26 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
28 #else: 27 #else:
29 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt 28 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
30 #end if 29 #end if
31 --scaleFactor $scaling.scaleFactor
32 #end if 30 #end if
33 31
34 #if str($region).strip() != '': 32 #if str($region).strip() != '':
35 --region '$region' 33 --region '$region'
36 #end if 34 #end if
37 35
38 #if $advancedOpt.showAdvancedOpt == "yes": 36 #if $advancedOpt.showAdvancedOpt == "yes":
37 #if str($advancedOpt.scaleFactor).strip() != '':
38 --scaleFactor $advancedOpt.scaleFactor
39 #end if
40
39 #if $advancedOpt.smoothLength: 41 #if $advancedOpt.smoothLength:
40 --smoothLength '$advancedOpt.smoothLength' 42 --smoothLength '$advancedOpt.smoothLength'
41 #end if 43 #end if
42 44
43 @ADVANCED_OPTS_READ_PROCESSING@ 45 @ADVANCED_OPTS_READ_PROCESSING@
72 <param name="type" type="select" label="Scaling/Normalization method" > 74 <param name="type" type="select" label="Scaling/Normalization method" >
73 <option value="1x">Normalize coverage to 1x</option> 75 <option value="1x">Normalize coverage to 1x</option>
74 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option> 76 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
75 <option value="no">Do not normalize or scale</option> 77 <option value="no">Do not normalize or scale</option>
76 </param> 78 </param>
77 <when value="rpkm"> 79 <when value="rpkm"/>
78 <expand macro="scaleFactor" />
79 </when>
80 <when value="no"/> 80 <when value="no"/>
81 <when value="1x"> 81 <when value="1x">
82 <expand macro="effectiveGenomeSize" /> 82 <expand macro="effectiveGenomeSize" />
83 <expand macro="scaleFactor" />
84 </when> 83 </when>
85 </conditional> 84 </conditional>
86 85
87 <param name="outFileFormat" type="select" label="Coverage file format"> 86 <param name="outFileFormat" type="select" label="Coverage file format">
88 <option value="bigwig" selected="true">bigwig</option> 87 <option value="bigwig" selected="true">bigwig</option>
96 <option value="no" selected="true">no</option> 95 <option value="no" selected="true">no</option>
97 <option value="yes">yes</option> 96 <option value="yes">yes</option>
98 </param> 97 </param>
99 <when value="no" /> 98 <when value="no" />
100 <when value="yes"> 99 <when value="yes">
100 <expand macro="scaleFactor" />
101 <expand macro="smoothLength" /> 101 <expand macro="smoothLength" />
102 102
103 <param argument="ignoreForNormalization" type="text" value="" 103 <param argument="ignoreForNormalization" type="text" value=""
104 label="Regions that should be excluded for normalization" 104 label="Regions that should be excluded for normalization"
105 help="A list of chromosome names separated by spaces 105 help="A list of chromosome names separated by spaces