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comparison bamCoverage.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
children
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29:3a2aab18a217 30:5231f398d784
1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description> 2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">bamCoverage</token> 4 <token name="@BINARY@">bamCoverage</token>
7 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
9 <command> 8 <command>
9 <![CDATA[
10 bamCoverage 10 bamCoverage
11 11
12 @THREADS@ 12 @THREADS@
13 13
14 --bam '$bamInput' 14 --bam '$bamInput'
15 --bamIndex ${bamInput.metadata.bam_index} 15 --bamIndex ${bamInput.metadata.bam_index}
16 --outFileName '$outFileName' 16 --outFileName '$outFileName'
17 --outFileFormat '$outFileFormat' 17 --outFileFormat '$outFileFormat'
18 18
19 --fragmentLength $fragmentLength 19 --fragmentLength $fragmentLength
20 --binSize $binSize 20 --binSize $binSize
21 21
22 #if $scaling.type=='rpkm': 22 #if $scaling.type=='rpkm':
23 --normalizeUsingRPKM 23 --normalizeUsingRPKM
24 #elif $scaling.type=='1x': 24 #elif $scaling.type=='1x':
25 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": 25 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
26 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize 26 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
27 #else: 27 #else:
28 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt 28 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
29 #end if 29 #end if
30 #elif $scaling.type=='own': 30 #elif $scaling.type=='own':
31 --scaleFactor $scaling.scaleFactor 31 --scaleFactor $scaling.scaleFactor
32 #end if
33
34 #if str($region).strip() != '':
35 --region '$region'
36 #end if
37
38 #if $advancedOpt.showAdvancedOpt == "yes":
39 #if $advancedOpt.smoothLength:
40 --smoothLength '$advancedOpt.smoothLength'
41 #end if 32 #end if
42 33
43 $advancedOpt.doNotExtendPairedEnds 34 #if str($region).strip() != '':
44 $advancedOpt.ignoreDuplicates 35 --region '$region'
45
46 #if $advancedOpt.minMappingQuality:
47 --minMappingQuality '$advancedOpt.minMappingQuality'
48 #end if 36 #end if
49 37
50 --missingDataAsZero $advancedOpt.missingDataAsZero 38 #if $advancedOpt.showAdvancedOpt == "yes":
39 #if $advancedOpt.smoothLength:
40 --smoothLength '$advancedOpt.smoothLength'
41 #end if
51 42
52 ##if str($advancedOpt.ignoreForNormalization).strip() != '': 43 $advancedOpt.doNotExtendPairedEnds
53 ## --ignoreForNormalization $advancedOpt.ignoreForNormalization 44 $advancedOpt.ignoreDuplicates
54 ##end if
55 45
56 #end if 46 #if $advancedOpt.minMappingQuality:
47 --minMappingQuality '$advancedOpt.minMappingQuality'
48 #end if
49
50 --missingDataAsZero $advancedOpt.missingDataAsZero
51
52 ##if str($advancedOpt.ignoreForNormalization).strip() != '':
53 ## --ignoreForNormalization $advancedOpt.ignoreForNormalization
54 ##end if
55 #if $samFlag:
56 --samFlag $samFlag
57 #end if
58 #end if
59 ]]>
57 </command> 60 </command>
58 61
59 <inputs> 62 <inputs>
60 <param name="bamInput" format="bam" type="data" label="BAM file" 63 <param name="bamInput" format="bam" type="data" label="BAM file"
61 help="The BAM file must be sorted."/> 64 help="The BAM file must be sorted."/>
62 65
63 <param name="fragmentLength" type="integer" value="300" min="1" 66 <param name="fragmentLength" type="integer" value="200" min="1"
64 label="Length of the average fragment size" 67 label="Length of the average fragment size"
65 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> 68 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length. (--fragmentLength)"/>
66 69
67 <param name="binSize" type="integer" value="50" min="1" 70 <param name="binSize" type="integer" value="50" min="1"
68 label="Bin size in bp" 71 label="Bin size in bp"
69 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/> 72 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
70 73
100 </param> 103 </param>
101 <when value="no" /> 104 <when value="no" />
102 <when value="yes"> 105 <when value="yes">
103 <param name="smoothLength" type="integer" value="1" optional="true" min="1" 106 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
104 label="Smooth values using the following length (in bp)" 107 label="Smooth values using the following length (in bp)"
105 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> 108 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied. (--smoothLength)"/>
106 109
107 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 110 <expand macro="doNotExtendPairedEnds" />
108 label="Do not extend paired ends" 111 <expand macro="ignoreDuplicates" />
109 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> 112 <expand macro="minMappingQuality" />
110
111 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
112 label="Ignore duplicates"
113 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
114
115 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
116 label="Minimum mapping quality"
117 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
118
119 <expand macro="missingDataAsZero" /> 113 <expand macro="missingDataAsZero" />
120 114 <expand macro="samFlag" />
121 <!-- <param name="ignoreForNormalization" type="text" value="" size="50" 115 <!-- <param name="ignoreForNormalization" type="text" value="" size="50"
122 label="regions that should be excluded for calculating the scaling factor" 116 label="regions that should be excluded for calculating the scaling factor"
123 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" /> 117 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
124 --> 118 -->
125 </when> 119 </when>
131 <when input="outFileFormat" value="bigwig" format="bigwig" /> 125 <when input="outFileFormat" value="bigwig" format="bigwig" />
132 <when input="outFileFormat" value="bedgraph" format="bedgraph" /> 126 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
133 </change_format> 127 </change_format>
134 </data> 128 </data>
135 </outputs> 129 </outputs>
130 <tests>
131 <test>
132 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
133 <param name="outFileFormat" value="bigwig" />
134 <param name="showAdvancedOpt" value="no" />
135 <param name="binSize" value="10" />
136 <param name="type" value="no" />
137 <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
138 </test>
139 <test>
140 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
141 <param name="outFileFormat" value="bigwig" />
142 <param name="showAdvancedOpt" value="no" />
143 <param name="binSize" value="10" />
144 <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
145 </test>
146 <test>
147 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
148 <param name="outFileFormat" value="bedgraph" />
149 <param name="showAdvancedOpt" value="no" />
150 <param name="binSize" value="10" />
151 <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
152 </test>
153 <test>
154 <param name="bamInput" value="phiX.bam" ftype="bam" />
155 <param name="outFileFormat" value="bigwig" />
156 <param name="showAdvancedOpt" value="no" />
157 <param name="binSize" value="10" />
158 <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
159 </test>
160 <test>
161 <param name="bamInput" value="phiX.bam" ftype="bam" />
162 <param name="outFileFormat" value="bedgraph" />
163 <param name="showAdvancedOpt" value="no" />
164 <param name="binSize" value="10" />
165 <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
166 </test>
167 </tests>
136 <help> 168 <help>
137 169 <![CDATA[
138 **What it does** 170 **What it does**
139 171
140 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or 172 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
141 read coverages. The way the method works is by first calculating all the 173 read coverages. The way the method works is by first calculating all the
142 number of reads (either extended to match the fragment length or not) that 174 number of reads (either extended to match the fragment length or not) that
158 - coverage file either in bigWig or bedGraph format 190 - coverage file either in bigWig or bedGraph format
159 191
160 ----- 192 -----
161 193
162 @REFERENCES@ 194 @REFERENCES@
163 195 ]]>
164 </help> 196 </help>
165 <expand macro="citations" /> 197 <expand macro="citations" />
166 </tool> 198 </tool>