Mercurial > repos > bgruening > deeptools_bam_coverage

comparison bamCoverage.xml @ 8:028fcce954f1 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
author bgruening
date Mon, 19 Sep 2016 18:05:26 -0400
parents 115aa2cbf152
children aa33302db115
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7:65e0795278b4 8:028fcce954f1
48 #end if 48 #end if
49 49
50 #if str($advancedOpt.filterRNAstrand) != 'no': 50 #if str($advancedOpt.filterRNAstrand) != 'no':
51 --filterRNAstrand '$advancedOpt.filterRNAstrand' 51 --filterRNAstrand '$advancedOpt.filterRNAstrand'
52 #end if 52 #end if
53
54 #if $advancedOpt.Offset:
55 --Offset '$advancedOpt.Offset'
56 #end if
57
58 @blacklist@
53 #end if 59 #end if
54 ]]> 60 ]]>
55 </command> 61 </command>
56 62
57 <inputs> 63 <inputs>
105 <expand macro="skipNAs" /> 111 <expand macro="skipNAs" />
106 <expand macro="read_processing_options" /> 112 <expand macro="read_processing_options" />
107 113
108 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue="" 114 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
109 label="Determine nucleosome positions from MNase-seq data" 115 label="Determine nucleosome positions from MNase-seq data"
110 help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." /> 116 help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options." />
117
118 <param argument="--Offset" type="integer" value="" optional="True"
119 label="Offset inside each alignment to use for the signal location."
120 help="Uses this offset inside of each read as the signal. This is useful in
121 cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
122 should be used to denote where the signal is (rather than the span of the
123 whole alignment). This can be paired with the --filterRNAstrand option. Note
124 that negative values indicate offsets from the end of each read. A value of
125 1 indicates the first base of the alignment (taking alignment orientation
126 into account). Likewise, a value of -1 is the last base of the alignment. An
127 offset of 0 is not permitted. By default, the entire alignment is used to
128 denote where the signal is located." />
111 129
112 <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 130 <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
113 help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands. 131 help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
114 Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented."> 132 Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
115 <option value="no" selected="true">no</option> 133 <option value="no" selected="true">no</option>
116 <option value="forward">forward</option> 134 <option value="forward">forward</option>
117 <option value="reverse">reverse</option> 135 <option value="reverse">reverse</option>
118 </param> 136 </param>
137 <expand macro="blacklist" />
119 138
120 </when> 139 </when>
121 </conditional> 140 </conditional>
122 </inputs> 141 </inputs>
123 <outputs> 142 <outputs>