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comparison bamCoverage.xml @ 10:aa33302db115 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 08:08:15 -0500
parents 028fcce954f1
children 22bfbb186bf1
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9:e22b1110529c 10:aa33302db115
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 53
54 #if $advancedOpt.Offset: 54 #if $advancedOpt.Offset:
55 --Offset '$advancedOpt.Offset' 55 --Offset $advancedOpt.Offset
56 #end if 56 #end if
57 57
58 @blacklist@ 58 @blacklist@
59 #end if 59 #end if
60 ]]> 60 ]]>
113 113
114 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue="" 114 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
115 label="Determine nucleosome positions from MNase-seq data" 115 label="Determine nucleosome positions from MNase-seq 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." /> 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." />
117 117
118 <param argument="--Offset" type="integer" value="" optional="True" 118 <param argument="--Offset" type="text" value="" optional="True"
119 label="Offset inside each alignment to use for the signal location." 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 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 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 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 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 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 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 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 127 offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
128 denote where the signal is located." /> 128 used to specify a range of positions. Note that specifying something like
129 --Offset 5 -1 will result in the 5th through last position being used, which
130 is equivalent to trimming 4 bases from the 5-prime end of alignments." />
129 131
130 <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 132 <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
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. 133 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.
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."> 134 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.">
133 <option value="no" selected="true">no</option> 135 <option value="no" selected="true">no</option>
190 <param name="showAdvancedOpt" value="yes" /> 192 <param name="showAdvancedOpt" value="yes" />
191 <param name="filterRNAstrand" value="reverse" /> 193 <param name="filterRNAstrand" value="reverse" />
192 <param name="binSize" value="10" /> 194 <param name="binSize" value="10" />
193 <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" /> 195 <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
194 </test> 196 </test>
197 <test>
198 <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
199 <param name="outFileFormat" value="bigwig" />
200 <param name="showAdvancedOpt" value="yes" />
201 <param name="binSize" value="10" />
202 <param name="Offset" value="-4 -1" />
203 <param name="doExtend" value="yes" />
204 <param name="minMappingQuality" value="0" />
205 <param name="type" value="no" />
206 <output name="outFileName" file="bamCoverage_result6.bw" ftype="bigwig" />
207 </test>
195 </tests> 208 </tests>
196 <help> 209 <help>
197 <![CDATA[ 210 <![CDATA[
198 211
199 What it does 212 What it does