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comparison bamCoverage.xml @ 0:19a6007845cc draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:19:01 -0500
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children 36f655a04a57
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1 <tool id="deeptools_bam_coverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
2 <description>generates a coverage bigWig file from a given BAM file</description>
3 <macros>
4 <token name="@BINARY@">bamCoverage</token>
5 <import>deepTools_macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 <![CDATA[
10 ln -s '$bamInput' one.bam &&
11 ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
12
13 @BINARY@
14 @THREADS@
15
16 --bam one.bam
17 --outFileName '$outFileName'
18 --outFileFormat '$outFileFormat'
19
20 --binSize $binSize
21
22 #if $scaling.type=='rpkm':
23 --normalizeUsingRPKM
24 #elif $scaling.type=='1x':
25 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
26 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
27 #else:
28 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
29 #end if
30 #elif $scaling.type=='own':
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
42
43 @ADVANCED_OPTS_READ_PROCESSING@
44 $advancedOpt.skipNAs
45
46 #if str($advancedOpt.ignoreForNormalization).strip() != '':
47 --ignoreForNormalization $advancedOpt.ignoreForNormalization
48 #end if
49 #end if
50 ]]>
51 </command>
52
53 <inputs>
54 <param name="bamInput" format="bam" type="data" label="BAM file"
55 help="The BAM file must be sorted."/>
56
57 <param name="binSize" type="integer" value="50" min="1"
58 label="Bin size in bases"
59 help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
60
61 <conditional name="scaling">
62 <param name="type" type="select" label="Scaling/Normalization method" >
63 <option value="1x">Normalize coverage to 1x</option>
64 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
65 <option value="no">Do not normalize or scale</option>
66 </param>
67 <when value="rpkm">
68 <expand macro="scaleFactor" />
69 </when>
70 <when value="no"/>
71 <when value="1x">
72 <expand macro="effectiveGenomeSize" />
73 <expand macro="scaleFactor" />
74 </when>
75 </conditional>
76
77 <param name="outFileFormat" type="select" label="Coverage file format">
78 <option value="bigwig" selected="true">bigwig</option>
79 <option value="bedgraph">bedgraph</option>
80 </param>
81
82 <expand macro="region_limit_operation" />
83
84 <conditional name="advancedOpt">
85 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
86 <option value="no" selected="true">no</option>
87 <option value="yes">yes</option>
88 </param>
89 <when value="no" />
90 <when value="yes">
91 <expand macro="smoothLength" />
92
93 <param argument="ignoreForNormalization" type="text" value=""
94 label="Regions that should be excluded for normalization"
95 help="A list of chromosome names separated by spaces
96 containing those chromosomes that should be excluded
97 during normalization. This is useful when
98 considering samples with unequal coverage across
99 chromosomes, like male and female samples. Example: chrX chrM" />
100
101 <expand macro="skipNAs" />
102 <expand macro="read_processing_options" />
103
104 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
105 label="Determine nucleosome positions from MNase-seq data"
106 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." />
107
108 </when>
109 </conditional>
110 </inputs>
111 <outputs>
112 <data format="bigwig" name="outFileName">
113 <change_format>
114 <when input="outFileFormat" value="bigwig" format="bigwig" />
115 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
116 </change_format>
117 </data>
118 </outputs>
119 <tests>
120 <test>
121 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
122 <param name="outFileFormat" value="bigwig" />
123 <param name="showAdvancedOpt" value="no" />
124 <param name="binSize" value="10" />
125 <param name="type" value="no" />
126 <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
127 </test>
128 <test>
129 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
130 <param name="outFileFormat" value="bigwig" />
131 <param name="showAdvancedOpt" value="no" />
132 <param name="binSize" value="10" />
133 <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
134 </test>
135 <test>
136 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
137 <param name="outFileFormat" value="bedgraph" />
138 <param name="showAdvancedOpt" value="no" />
139 <param name="binSize" value="10" />
140 <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
141 </test>
142 <test>
143 <param name="bamInput" value="phiX.bam" ftype="bam" />
144 <param name="outFileFormat" value="bigwig" />
145 <param name="showAdvancedOpt" value="no" />
146 <param name="binSize" value="10" />
147 <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
148 </test>
149 <test>
150 <param name="bamInput" value="phiX.bam" ftype="bam" />
151 <param name="outFileFormat" value="bedgraph" />
152 <param name="showAdvancedOpt" value="yes" />
153 <param name="binSize" value="10" />
154 <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
155 </test>
156 </tests>
157 <help>
158 <![CDATA[
159 **What it does**
160
161 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
162 read coverages. The way the method works is by first calculating all the
163 number of reads (either extended to match the fragment length or not) that
164 overlap each bin in the genome. The resulting read counts can be normalized
165 using either a given scaling factor, the RPKM formula or to get a 1x depth of
166 coverage (RPGC). In the case of paired-end mapping, each read mate is treated
167 independently to avoid a bias when a mixture of concordant and discordant
168 pairs is present. This means that *each end* will be extended to match the
169 fragment length.
170
171 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
172
173
174 You can find more details on the bamCoverage doc page: https://deeptools.readthedocs.org/en/master/content/tools/bamCoverage.html
175
176
177 **Output files**:
178
179 - coverage file either in bigWig or bedGraph format
180
181 -----
182
183 @REFERENCES@
184 ]]>
185 </help>
186 <expand macro="citations" />
187 </tool>